MSX2 (msh homeobox 2) - Rat Genome Database

Name: MSX2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: MSX2 (msh homeobox 2) Homo sapiens

Analyze

Symbol:

MSX2

Name:

msh homeobox 2

RGD ID:

735997

HGNC Page

HGNC

Description:

Enables sequence-specific double-stranded DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in cytosol and nuclear speck. Implicated in craniosynostosis and parietal foramina.

Type:

protein-coding

RefSeq Status:

REVIEWED

Previously known as:

CRS2; FPP; homeobox protein Hox-8; homeobox protein MSX-2; HOX8; MSH; msh homeo box 2; msh homeo box homolog 2 (drosophila); msh homeobox homolog 2; PFM; PFM1

RGD Orthologs

Mouse

Rat

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Mus musculus (house mouse):	Msx2 (msh homeobox 2)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Rattus norvegicus (Norway rat):	Msx2 (msh homeobox 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Chinchilla lanigera (long-tailed chinchilla):	Msx2 (msh homeobox 2)	NCBI	Ortholog
Pan paniscus (bonobo/pygmy chimpanzee):	MSX2 (msh homeobox 2)	NCBI	Ortholog
Canis lupus familiaris (dog):	MSX2 (msh homeobox 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Msx2 (msh homeobox 2)	NCBI	Ortholog
Sus scrofa (pig):	MSX2 (msh homeobox 2)	HGNC	Ensembl, NCBI, OrthoDB
Chlorocebus sabaeus (green monkey):	MSX2 (msh homeobox 2)	NCBI	Ortholog
Heterocephalus glaber (naked mole-rat):	Msx2 (msh homeobox 2)	NCBI	Ortholog
Other homologs ²
Mus musculus (house mouse):	Msx1 (msh homeobox 1)	HGNC	OrthoDB
Canis lupus familiaris (dog):	MSX1 (msh homeobox 1)	HGNC	OrthoDB
Sus scrofa (pig):	MSX1 (msh homeobox 1)	HGNC	OrthoDB
Alliance orthologs ³
Rattus norvegicus (Norway rat):	Msx2 (msh homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|sonicParanoid)
Mus musculus (house mouse):	Msx2 (msh homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|sonicParanoid)
Danio rerio (zebrafish):	msx2b (muscle segment homeobox 2b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|ZFIN\|sonicParanoid)
Danio rerio (zebrafish):	msx2a (muscle segment homeobox 2a)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|ZFIN)
Drosophila melanogaster (fruit fly):	Dr	Alliance	DIOPT (Hieranoid\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	vab-15	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|sonicParanoid)

Related Pseudogenes:

MSX2P1

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	174,724,582 - 174,730,896 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	5	174,724,582 - 174,730,896 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	5	174,151,585 - 174,157,899 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	174,084,181 - 174,090,508 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	174,084,207 - 174,090,507	NCBI
Celera	5	170,185,579 - 170,191,910 (+)	NCBI
Cytogenetic Map	5	q35.2	NCBI
HuRef	5	169,246,978 - 169,253,303 (+)	NCBI		HuRef
CHM1_1	5	173,583,988 - 173,590,298 (+)	NCBI		CHM1_1

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Craniofacial Abnormalities (EXP,IAGP)

craniosynostosis (IAGP,IEA,ISS)

Craniosynostosis 2 (IAGP)

Craniosynostosis Syndrome, Autosomal Recessive (IAGP)

Female Urogenital Diseases (EXP)

Femoral Fractures (ISO)

hypertension (ISO)

parietal foramina (EXP,IAGP)

Parietal Foramina 1 (IAGP)

Parietal Foramina with Cleidocranial Dysplasia (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP,ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,6-dinitrotoluene (ISO)

2-ethylhexan-1-ol (ISO)

3,7-dihydropurine-6-thione (ISO)

4,4'-sulfonyldiphenol (ISO)

5-fluorouracil (EXP)

acrylamide (ISO)

aflatoxin B1 (EXP)

all-trans-retinoic acid (EXP,ISO)

ammonium chloride (ISO)

arsenite(3-) (EXP)

arsenous acid (EXP)

belinostat (EXP)

benzalkonium chloride (ISO)

benzo[a]pyrene (EXP,ISO)

benzo[e]pyrene (EXP)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (ISO)

cadmium sulfate (ISO)

calcitriol (EXP)

carbamazepine (EXP)

carbon nanotube (ISO)

cobalt dichloride (EXP)

copper atom (ISO)

copper(0) (ISO)

coumestrol (EXP)

Cuprizon (ISO)

deoxynivalenol (EXP)

dexamethasone (ISO)

diarsenic trioxide (EXP)

diethylstilbestrol (ISO)

dioxygen (EXP)

dorsomorphin (EXP)

doxorubicin (EXP)

entinostat (EXP)

folic acid (ISO)

furan (ISO)

genistein (ISO)

glycerol 2-phosphate (ISO)

hexaconazole (ISO)

L-ascorbic acid (ISO)

lead diacetate (ISO)

lipopolysaccharide (ISO)

manganese(II) chloride (ISO)

mercaptopurine (ISO)

mercury dibromide (EXP)

methapyrilene (EXP)

methylmercury chloride (EXP)

Muraglitazar (ISO)

N-methyl-4-phenylpyridinium (ISO)

N-nitrosodiethylamine (ISO)

p-chloromercuribenzoic acid (EXP)

panobinostat (EXP)

phenethyl caffeate (ISO)

phenylmercury acetate (EXP)

potassium phosphate (ISO)

progesterone (ISO)

purine-6-thiol (ISO)

retinyl acetate (ISO)

SB 431542 (EXP)

silicon dioxide (EXP)

sunitinib (EXP)

tebuconazole (EXP)

Tesaglitazar (ISO)

triadimefon (ISO)

trichostatin A (EXP)

troglitazone (ISO)

valproic acid (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of meiosis (IEA,ISO)

anterior/posterior pattern specification (IEA,ISO)

BMP signaling pathway (IEA,ISO)

BMP signaling pathway involved in heart development (IEA,ISO)

bone morphogenesis (IEA,ISO)

bone trabecula formation (IEA,ISO)

branching involved in mammary gland duct morphogenesis (IEA,ISO)

cardiac conduction system development (NAS)

cartilage development (IEA,ISO)

cellular response to estradiol stimulus (IEA,ISO)

cellular response to growth factor stimulus (IEA,ISO)

chondrocyte development (IEA,ISO)

cranial suture morphogenesis (TAS)

embryonic digit morphogenesis (IEA,ISO)

embryonic forelimb morphogenesis (IEA,ISO)

embryonic hindlimb morphogenesis (IEA,ISO)

embryonic limb morphogenesis (IEA,ISO)

embryonic morphogenesis (IBA)

embryonic nail plate morphogenesis (IEA,ISO)

enamel mineralization (IEA,ISO)

endochondral bone growth (IEA,ISO)

epithelial to mesenchymal transition involved in endocardial cushion formation (IEA,ISO)

frontal suture morphogenesis (IEA,ISO)

mammary gland epithelium development (IEA,ISO)

mesenchymal cell apoptotic process (IEA,ISO)

negative regulation of apoptotic process (IEA,ISO)

negative regulation of cell population proliferation (IEA,ISO)

negative regulation of CREB transcription factor activity (IEA,ISO)

negative regulation of fat cell differentiation (IEA,ISO)

negative regulation of keratinocyte differentiation (IEA,ISO)

negative regulation of transcription by RNA polymerase II (IEA,IMP,ISO,ISS)

negative regulation of transcription regulatory region DNA binding (IEA,ISO,ISS)

negative regulation of transcription, DNA-templated (IEA,ISS)

odontogenesis (IEA,ISO)

ossification (IEA,ISO)

osteoblast development (IEA,ISO)

osteoblast differentiation (IEA,ISS)

outflow tract morphogenesis (IEA,ISO)

outflow tract septum morphogenesis (IEA,ISO)

positive regulation of apoptotic process (ISO)

positive regulation of BMP signaling pathway (IEA,ISO)

positive regulation of cell death (ISO)

positive regulation of mesenchymal cell apoptotic process (IEA,ISO)

positive regulation of osteoblast differentiation (IEA,ISO)

positive regulation of timing of catagen (IEA,ISO)

regulation of apoptotic process (IEA,ISO)

regulation of transcription by RNA polymerase II (IBA)

regulation of transcription, DNA-templated (IEA)

signal transduction involved in regulation of gene expression (IEA,ISO)

stem cell differentiation (IEA,ISO)

transcription by RNA polymerase II (ISO)

wound healing (IEA,ISO)

wound healing, spreading of epidermal cells (IEA,ISO)

Cellular Component

chromatin (ISA)

cytosol (IDA)

nuclear speck (IDA)

nucleus (IBA,IEA)

transcription regulator complex (IEA)

Molecular Function

DNA binding (IEA)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA,IEA,ISA,ISO,ISS)

DNA-binding transcription repressor activity, RNA polymerase II-specific (IEA)

protein binding (IPI)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (IBA,IEA)

sequence-specific DNA binding (IDA)

sequence-specific double-stranded DNA binding (IDA)

transcription cis-regulatory region binding (IEA,ISS)

Phenotype Annotations Click to see Annotation Detail View

Human Phenotype

Abnormal cerebral vein morphology (IAGP)

Abnormal posterior cranial fossa morphology (IAGP)

Aplasia cutis congenita of scalp (IAGP)

Autosomal dominant inheritance (IAGP)

Bicoronal synostosis (IAGP)

Brachydactyly (IAGP)

Brachyturricephaly (IAGP)

Broad thumb (IAGP)

Cleft lip (IAGP)

Cleft palate (IAGP)

Cleft soft palate (IAGP)

Cleft upper lip (IAGP)

Congenital craniofacial dysostosis (IAGP)

Craniosynostosis (IAGP)

Cranium bifidum occultum (IAGP)

Dermoid cyst (IAGP)

Encephalocele (IAGP)

Encephalomalacia (IAGP)

Frontal bossing (IAGP)

Headache (IAGP)

Heterogeneous (IAGP)

Hypermetropia (IAGP)

Hypotelorism (IAGP)

Intellectual disability (IAGP)

Macrocephaly (IAGP)

Microtia (IAGP)

Multiple exostoses (IAGP)

Myelomeningocele (IAGP)

Myopia (IAGP)

Occipital encephalocele (IAGP)

Parietal foramina (IAGP)

Scalp tenderness (IAGP)

Seizure (IAGP)

Short clavicles (IAGP)

Supernumerary tooth (IAGP)

Symmetrical, oval parietal bone defects (IAGP)

Trigonocephaly (IAGP)

Triphalangeal thumb (IAGP)

Unicoronal synostosis (IAGP)

Venous malformation (IAGP)

Visual field defect (IAGP)

Vomiting (IAGP)

Widely patent fontanelles and sutures (IAGP)

References

References - curated


1.	GOA_HUMAN data from the GO Consortium
2.	Johnston JD, etal., J Neuroendocrinol. 2006 Jan;18(1):50-6.
3.	Kanemaru K, etal., J Pharmacol Sci. 2008 Feb;106(2):280-6. Epub 2008 Feb 9.
4.	Ma L, etal., Hum Mol Genet. 1996 Dec;5(12):1915-20.
5.	OMIM Disease Annotation Pipeline
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	RGD automated import pipeline for human HPO-to-gene-to-disease annotations
9.	Wilkie AO, etal., Nat Genet. 2000 Apr;24(4):387-90.

Additional References at PubMed

PMID:7687426	PMID:7726844	PMID:7897272	PMID:8101453	PMID:8106171	PMID:8668339	PMID:8786091	PMID:9073066	PMID:9111364	PMID:9256341	PMID:9265625	PMID:9373945
PMID:9522127	PMID:10451362	PMID:10767351	PMID:10831122	PMID:11084035	PMID:11683913	PMID:11763998	PMID:11959851	PMID:12145306	PMID:12145307	PMID:12145310	PMID:12407713
PMID:12477932	PMID:12750290	PMID:12925529	PMID:14571277	PMID:14671321	PMID:14679154	PMID:15060165	PMID:15489334	PMID:16327884	PMID:16425399	PMID:16467978	PMID:16540516
PMID:16642368	PMID:17693062	PMID:18029348	PMID:18056036	PMID:18187185	PMID:18299954	PMID:18349132	PMID:18786927	PMID:19147956	PMID:19240061	PMID:19274049	PMID:19407244
PMID:19453261	PMID:19590514	PMID:19835636	PMID:20004646	PMID:20107842	PMID:20211142	PMID:20301307	PMID:20506112	PMID:20538960	PMID:20572854	PMID:20620318	PMID:20634891
PMID:20672350	PMID:20682066	PMID:21362336	PMID:21465479	PMID:21471203	PMID:21498730	PMID:21499300	PMID:21512281	PMID:21730974	PMID:21873635	PMID:22332551	PMID:22633971
PMID:22717651	PMID:22730815	PMID:23275563	PMID:23949913	PMID:24549638	PMID:24666290	PMID:26186194	PMID:26427715	PMID:26786210	PMID:27088357	PMID:28286778	PMID:28473536
PMID:28514442	PMID:28933666	PMID:29860758	PMID:30341511	PMID:30779868	PMID:31548378	PMID:32210188	PMID:32248833	PMID:32296183	PMID:32393512	PMID:32814053	PMID:33731348
PMID:33958655	PMID:33961781	PMID:34435915

Genomics

Comparative Map Data

MSX2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	174,724,582 - 174,730,896 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	5	174,724,582 - 174,730,896 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	5	174,151,585 - 174,157,899 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	174,084,181 - 174,090,508 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	174,084,207 - 174,090,507	NCBI
Celera	5	170,185,579 - 170,191,910 (+)	NCBI
Cytogenetic Map	5	q35.2	NCBI
HuRef	5	169,246,978 - 169,253,303 (+)	NCBI		HuRef
CHM1_1	5	173,583,988 - 173,590,298 (+)	NCBI		CHM1_1

Msx2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	53,620,917 - 53,626,816 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	13	53,620,920 - 53,627,110 (-)	Ensembl
GRCm38	13	53,466,881 - 53,472,780 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	53,466,884 - 53,473,074 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	13	53,562,250 - 53,568,149 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	13	53,475,420 - 53,480,608 (-)	NCBI			mm8
Celera	13	54,545,172 - 54,551,024 (-)	NCBI		Celera
Cytogenetic Map	13	B1	NCBI
cM Map	13	27.84	NCBI

Msx2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	17	11,097,214 - 11,102,879 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	17	11,097,103 - 11,102,879 (+)	Ensembl
Rnor_6.0	17	11,683,862 - 11,689,527 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	17	11,683,862 - 11,689,527 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	17	13,785,024 - 13,790,689 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	17,243,262 - 17,248,927 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	17	17,247,335 - 17,247,755 (+)	NCBI
Celera	17	11,158,359 - 11,164,024 (+)	NCBI		Celera
RH 3.4 Map	17	109.2	RGD
Cytogenetic Map	17	p14	NCBI

Msx2
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955408	27,323,360 - 27,329,755 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955408	27,323,405 - 27,329,484 (+)	NCBI	ChiLan1.0	ChiLan1.0

MSX2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	5	176,968,315 - 176,974,679 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	176,967,902 - 176,976,609 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	170,063,137 - 170,070,226 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

MSX2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	4	38,002,724 - 38,007,407 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	4	38,002,428 - 38,007,407 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	4	37,948,799 - 37,953,445 (-)	NCBI
ROS_Cfam_1.0	4	38,376,184 - 38,380,830 (-)	NCBI
ROS_Cfam_1.0 Ensembl	4	38,375,888 - 38,381,225 (-)	Ensembl
UMICH_Zoey_3.1	4	38,192,821 - 38,197,476 (-)	NCBI
UNSW_CanFamBas_1.0	4	38,380,991 - 38,385,645 (-)	NCBI
UU_Cfam_GSD_1.0	4	38,891,167 - 38,895,822 (-)	NCBI

Msx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024407213	92,492,782 - 92,498,921 (-)	NCBI
SpeTri2.0	NW_004936609	1,216,436 - 1,221,528 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

MSX2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	16	49,766,897 - 49,771,634 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	16	49,765,587 - 49,771,745 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

MSX2
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	23	76,873,499 - 76,879,935 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	23	76,873,669 - 76,879,553 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666034	1,717,428 - 1,723,746 (-)	NCBI	Vero_WHO_p1.0

Msx2
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624733	15,288,417 - 15,294,481 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

RH119225

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	5	174,153,104 - 174,153,437	UniSTS	GRCh37
Build 36	5	174,085,710 - 174,086,043	RGD	NCBI36
Celera	5	170,187,108 - 170,187,441	RGD
Cytogenetic Map	5	q35.2	UniSTS
HuRef	5	169,248,507 - 169,248,840	UniSTS
TNG Radiation Hybrid Map	5	82208.0	UniSTS

GDB:266598

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	5	174,155,856 - 174,156,054	UniSTS	GRCh37
Build 36	5	174,088,462 - 174,088,660	RGD	NCBI36
Celera	5	170,189,861 - 170,190,061	RGD
Cytogenetic Map	5	q35.2	UniSTS
HuRef	5	169,251,260 - 169,251,454	UniSTS

PMC164857P2

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	17	56,234,746 - 56,235,165	UniSTS	GRCh37
GRCh37	5	174,156,167 - 174,156,586	UniSTS	GRCh37
Build 36	5	174,088,773 - 174,089,192	RGD	NCBI36
Celera	17	52,696,525 - 52,696,944	UniSTS
Celera	5	170,190,174 - 170,190,593	RGD
Cytogenetic Map	5	q35.2	UniSTS
Cytogenetic Map	17	q22	UniSTS
HuRef	17	51,595,564 - 51,595,983	UniSTS
HuRef	5	169,251,567 - 169,251,986	UniSTS

MSX2_1676

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	5	174,156,261 - 174,157,073	UniSTS	GRCh37
Build 36	5	174,088,867 - 174,089,679	RGD	NCBI36
Celera	5	170,190,268 - 170,191,080	RGD
HuRef	5	169,251,661 - 169,252,473	UniSTS

SHGC-11995

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	5	174,156,626 - 174,156,744	UniSTS	GRCh37
Build 36	5	174,089,232 - 174,089,350	RGD	NCBI36
Celera	5	170,190,633 - 170,190,751	RGD
Cytogenetic Map	5	q35.2	UniSTS
HuRef	5	169,252,026 - 169,252,144	UniSTS
Stanford-G3 RH Map	5	6151.0	UniSTS
GeneMap99-G3 RH Map	5	6239.0	UniSTS

RH79930

Human Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	5	q35.2	UniSTS
GeneMap99-GB4 RH Map	5	640.67	UniSTS

STS-X69295

Human Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	5	q35.2	UniSTS
GeneMap99-GB4 RH Map	5	640.77	UniSTS

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	584
Count of miRNA genes:	461
Interacting mature miRNAs:	489
Transcripts:	ENST00000239243, ENST00000507785
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system

circulatory system

endocrine system

exocrine system

hemolymphoid system

hepatobiliary system

integumental system

musculoskeletal system

nervous system

renal system

reproductive system

respiratory system

sensory system

visual system

adipose tissue

appendage

entire extraembryonic component

High

Medium

132

350

558

321

406

Low

1839

1676

731

173

432

3555

1979

1817

152

959

1224

151

1099

2201

Below cutoff

455

440

752

240

430

223

234

179

1692

182

160

262

101

180

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NG_008124	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_001363626	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_002449	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC117531	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AH004951	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL552909	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC015509	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BT009814	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH471062	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068273	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CS406127	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D14970	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D26145	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D31771	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D89377	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	S75308	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	S75361	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	W38629	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X69295	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENST00000239243 ⟹ ENSP00000239243

RefSeq Status:

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p13 Ensembl	5	174,724,582 - 174,730,896 (+)	Ensembl

RefSeq Acc Id:

ENST00000507785 ⟹ ENSP00000427425

RefSeq Status:

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p13 Ensembl	5	174,724,602 - 174,729,880 (+)	Ensembl

RefSeq Acc Id:

NM_001363626 ⟹ NP_001350555

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	5	174,724,582 - 174,730,896 (+)	NCBI

Sequence:

show sequence

GCAGCAAAAAAGTTTGAGTCGCCGCTGCCGGGTTGCCAGCGGAGTCGCGCGTCGGGAGCTACGT
AGGGCAGAGAAGTCATGGCTTCTCCGTCCAAAGGCAATGACTTGTTTTCGCCCGACGAGGAGGG
CCCAGCAGTGGTGGCCGGACCAGGCCCGGGGCCTGGGGGCGCCGAGGGGGCCGCGGAGGAGCGC
CGCGTCAAGGTCTCCAGCCTGCCCTTCAGCGTGGAGGCGCTCATGTCCGACAAGAAGCCGCCCA
AGGAGGCGTCCCCGCTGCCGGCCGAAAGCGCCTCGGCCGGGGCCACCCTGCGGCCACTGCTGCT
GTCGGGGCACGGCGCTCGGGAAGCGCACAGCCCCGGGCCGCTGGTGAAGCCCTTCGAGACCGCC
TCGGTCAAGTCGGAAAATTCAGAAGATGGAGCGGCGTGGATGCAGGAACCCGGCCGATATTCGC
CGCCGCCAAGTGAGTGCGCGCCGGGGCAGGAGTAGGAGGACATATGAGCCCTACCACCTGCACC
CTGAGGAAACACAAGACCAATCGGAAGCCGCGCACGCCCTTTACCACATCCCAGCTCCTCGCCC
TGGAGCGCAAGTTCCGTCAGAAACAGTACCTCTCCATTGCAGAGCGTGCAGAGTTCTCCAGCTC
TCTGAACCTCACAGAGACCCAGGTCAAAATCTGGTTCCAGAACCGAAGGGCCAAGGCGAAAAGA
CTGCAGGAGGCAGAACTGGAAAAGCTGAAAATGGCTGCAAAACCTATGCTGCCCTCCAGCTTCA
GTCTCCCTTTCCCCATCAGCTCGCCCCTGCAGGCAGCGTCCATATATGGAGCATCCTACCCGTT
CCATAGACCTGTGCTTCCCATCCCGCCTGTGGGACTCTATGCCACGCCAGTGGGATATGGCATG
TACCACCTGTCCTAAGGAAGACCAGATCAATAGACTCCATGATGGATGCTTGTTTCAAAGGGTT
TCCTCTCCCTCTCCACGAAGGCAGTACCAGCCAGTACTCCTGCTCTGCTAACCCTGCGTGCACC
ACCCTAAGCGGCTAGGCTGACAGGGCCACACGACATAGCTGAAATTTGTTCTGTAGGCGGAGGC
ACCAAGCCCTGTTTTCTTGGTGTAATCTTCCAGATGCCCCCTTTTCCTTTCACAAAGATTGGCT
CTGATGGTTTTTATGTATAAATATATATATATAATAAAATATAATACATTTTTATACAGCAGAC
GTAAAAATTCAAATTATTTTAAAAGGCAAAATTTATATACATATGTGCTTTTTTTCTATATCTC
ACCTTCCCAAAAGACACTGTGTAAGTCCATTTGTTGTATTTTCTTAAAGAGGGAGACAAATTAT
TTGCAAAATGTGCTAAAGTCAATGATTTTTACGGGATTATTGACTTCTGCTTATGGAAAACAAA
GAAACAGACACAATGCACACAGAAAATATTAGATATGGAGAGATTATTCAAAGTGAAGGGGACA
CATCATATTTCTGCATTTTACTTGCATTAAAAGAAACCTCTTTATATACTACAGTTGTTCCTAT
CTCTCCCCCGCCCCCCACCGCCCCACCACACACATATTTTTAAAGTTTTTCCTTTTTTAAGAAT
ATTTTTGTAAGACCAATACCTGGGATGAGAAGAATCCTGAGACTGCCTGGAGGTGAGGTAGAAA
ATTAGAAATACTTCCTAATTCTTCTCAAGGCTGTTGGTAACTTTATTTCAGATAATTGGAGAGT
AAAATGTTAAAACCTGTTGAGAGGAATTGATGGTTTCTGAGAAATACTAGGTACATTCATCCTC
ACAGATTGCAAAGGTGATTTGGGTGGGGGTTTAGTAATTTTCTGCTTAAAAAATGAGTATCTTG
TAACCATTACCTATATGCTAAATATTCTTGAACAATTAGTAGATCCAGAAAGAAAAAAAAATAT
GCTTTCTCTGTGTGTGTACCTGTTGTATGTCCTAAACTTATTAGAAAATTTTATATACTTTTTT
ACATGTTGGGGGGCAGAAGGTAAAGCCATGTTTTGACTTGGTGAAAATGGGATTGTCAAACAGC
CCATTAAGTTCCCTGGTATTTCACCTTCCTGTCCATCTGTCCCCTCCCTCCGGTATACCTTTAT
CCCTTTGAAAGGGTGCTTGTACAATTTGATATATTTTATTGAAGAGTTATCTCTTATTCTGAAT
TAAATTAAGCATTTGTTTTATTGCAGTAAAGTTTGTCCAAACTCACAA

hide sequence

RefSeq Acc Id:

NM_002449 ⟹ NP_002440

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	5	174,724,582 - 174,730,896 (+)	NCBI
GRCh37	5	174,151,575 - 174,157,902 (+)	ENTREZGENE
Build 36	5	174,084,181 - 174,090,508 (+)	NCBI Archive
HuRef	5	169,246,978 - 169,253,303 (+)	ENTREZGENE
CHM1_1	5	173,583,988 - 173,590,298 (+)	NCBI

Sequence:

show sequence

GCAGCAAAAAAGTTTGAGTCGCCGCTGCCGGGTTGCCAGCGGAGTCGCGCGTCGGGAGCTACGT
AGGGCAGAGAAGTCATGGCTTCTCCGTCCAAAGGCAATGACTTGTTTTCGCCCGACGAGGAGGG
CCCAGCAGTGGTGGCCGGACCAGGCCCGGGGCCTGGGGGCGCCGAGGGGGCCGCGGAGGAGCGC
CGCGTCAAGGTCTCCAGCCTGCCCTTCAGCGTGGAGGCGCTCATGTCCGACAAGAAGCCGCCCA
AGGAGGCGTCCCCGCTGCCGGCCGAAAGCGCCTCGGCCGGGGCCACCCTGCGGCCACTGCTGCT
GTCGGGGCACGGCGCTCGGGAAGCGCACAGCCCCGGGCCGCTGGTGAAGCCCTTCGAGACCGCC
TCGGTCAAGTCGGAAAATTCAGAAGATGGAGCGGCGTGGATGCAGGAACCCGGCCGATATTCGC
CGCCGCCAAGACATATGAGCCCTACCACCTGCACCCTGAGGAAACACAAGACCAATCGGAAGCC
GCGCACGCCCTTTACCACATCCCAGCTCCTCGCCCTGGAGCGCAAGTTCCGTCAGAAACAGTAC
CTCTCCATTGCAGAGCGTGCAGAGTTCTCCAGCTCTCTGAACCTCACAGAGACCCAGGTCAAAA
TCTGGTTCCAGAACCGAAGGGCCAAGGCGAAAAGACTGCAGGAGGCAGAACTGGAAAAGCTGAA
AATGGCTGCAAAACCTATGCTGCCCTCCAGCTTCAGTCTCCCTTTCCCCATCAGCTCGCCCCTG
CAGGCAGCGTCCATATATGGAGCATCCTACCCGTTCCATAGACCTGTGCTTCCCATCCCGCCTG
TGGGACTCTATGCCACGCCAGTGGGATATGGCATGTACCACCTGTCCTAAGGAAGACCAGATCA
ATAGACTCCATGATGGATGCTTGTTTCAAAGGGTTTCCTCTCCCTCTCCACGAAGGCAGTACCA
GCCAGTACTCCTGCTCTGCTAACCCTGCGTGCACCACCCTAAGCGGCTAGGCTGACAGGGCCAC
ACGACATAGCTGAAATTTGTTCTGTAGGCGGAGGCACCAAGCCCTGTTTTCTTGGTGTAATCTT
CCAGATGCCCCCTTTTCCTTTCACAAAGATTGGCTCTGATGGTTTTTATGTATAAATATATATA
TATAATAAAATATAATACATTTTTATACAGCAGACGTAAAAATTCAAATTATTTTAAAAGGCAA
AATTTATATACATATGTGCTTTTTTTCTATATCTCACCTTCCCAAAAGACACTGTGTAAGTCCA
TTTGTTGTATTTTCTTAAAGAGGGAGACAAATTATTTGCAAAATGTGCTAAAGTCAATGATTTT
TACGGGATTATTGACTTCTGCTTATGGAAAACAAAGAAACAGACACAATGCACACAGAAAATAT
TAGATATGGAGAGATTATTCAAAGTGAAGGGGACACATCATATTTCTGCATTTTACTTGCATTA
AAAGAAACCTCTTTATATACTACAGTTGTTCCTATCTCTCCCCCGCCCCCCACCGCCCCACCAC
ACACATATTTTTAAAGTTTTTCCTTTTTTAAGAATATTTTTGTAAGACCAATACCTGGGATGAG
AAGAATCCTGAGACTGCCTGGAGGTGAGGTAGAAAATTAGAAATACTTCCTAATTCTTCTCAAG
GCTGTTGGTAACTTTATTTCAGATAATTGGAGAGTAAAATGTTAAAACCTGTTGAGAGGAATTG
ATGGTTTCTGAGAAATACTAGGTACATTCATCCTCACAGATTGCAAAGGTGATTTGGGTGGGGG
TTTAGTAATTTTCTGCTTAAAAAATGAGTATCTTGTAACCATTACCTATATGCTAAATATTCTT
GAACAATTAGTAGATCCAGAAAGAAAAAAAAATATGCTTTCTCTGTGTGTGTACCTGTTGTATG
TCCTAAACTTATTAGAAAATTTTATATACTTTTTTACATGTTGGGGGGCAGAAGGTAAAGCCAT
GTTTTGACTTGGTGAAAATGGGATTGTCAAACAGCCCATTAAGTTCCCTGGTATTTCACCTTCC
TGTCCATCTGTCCCCTCCCTCCGGTATACCTTTATCCCTTTGAAAGGGTGCTTGTACAATTTGA
TATATTTTATTGAAGAGTTATCTCTTATTCTGAATTAAATTAAGCATTTGTTTTATTGCAGTAA
AGTTTGTCCAAACTCACAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001350555	(Get FASTA)	NCBI Sequence Viewer
	NP_002440	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB33867	(Get FASTA)	NCBI Sequence Viewer
	AAB42178	(Get FASTA)	NCBI Sequence Viewer
	AAD14169	(Get FASTA)	NCBI Sequence Viewer
	AAH15509	(Get FASTA)	NCBI Sequence Viewer
	AAP88816	(Get FASTA)	NCBI Sequence Viewer
	BAA03611	(Get FASTA)	NCBI Sequence Viewer
	BAA06549	(Get FASTA)	NCBI Sequence Viewer
	BAA13949	(Get FASTA)	NCBI Sequence Viewer
	CAA49156	(Get FASTA)	NCBI Sequence Viewer
	CAL40519	(Get FASTA)	NCBI Sequence Viewer
	EAW61381	(Get FASTA)	NCBI Sequence Viewer
	EAW61382	(Get FASTA)	NCBI Sequence Viewer
	P35548	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_002440 ⟸ NM_002449
- Peptide Label:	isoform 1
- UniProtKB:	P35548 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MASPSKGNDLFSPDEEGPAVVAGPGPGPGGAEGAAEERRVKVSSLPFSVEALMSDKKPPKEASP LPAESASAGATLRPLLLSGHGAREAHSPGPLVKPFETASVKSENSEDGAAWMQEPGRYSPPPRH MSPTTCTLRKHKTNRKPRTPFTTSQLLALERKFRQKQYLSIAERAEFSSSLNLTETQVKIWFQN RRAKAKRLQEAELEKLKMAAKPMLPSSFSLPFPISSPLQAASIYGASYPFHRPVLPIPPVGLYA TPVGYGMYHLS hide sequence

RefSeq Acc Id:	NP_001350555 ⟸ NM_001363626
- Peptide Label:	isoform 2

RefSeq Acc Id:

ENSP00000427425 ⟸ ENST00000507785

RefSeq Acc Id:

ENSP00000239243 ⟸ ENST00000239243

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P35548-F1-model_v2	AlphaFold	P35548	1-267	view protein structure

Promoters

RGD ID:

6803379

Promoter ID:

HG_KWN:51828

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

HeLa_S3

Transcripts:

OTTHUMT00000252981

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	5	174,083,601 - 174,084,302 (+)	MPROMDB

RGD ID:

6871600

Promoter ID:

EPDNEW_H8964

Type:

initiation region

Name:

MSX2_1

Description:

msh homeobox 2

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	5	174,724,622 - 174,724,682	EPDNEW

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
NM_002449.5(MSX2):c.443C>A (p.Pro148His)	single nucleotide variant	Craniosynostosis 2 [RCV000018474]\|Enlarged parietal foramina [RCV001210266]	Chr5:174729222 [GRCh38] Chr5:174156225 [GRCh37] Chr5:5q35.2	pathogenic
MSX2, 6-BP DEL, NT475	deletion	Parietal foramina 1 [RCV000018475]	Chr5:5q34-q35	pathogenic
NM_002449.5(MSX2):c.515G>A (p.Arg172His)	single nucleotide variant	Parietal foramina 1 [RCV000018476]	Chr5:174729294 [GRCh38] Chr5:174156297 [GRCh37] Chr5:5q35.2	pathogenic
nsv513767	deletion	Parietal foramina 1 [RCV000018477]	Chr5:5q34-q35	pathogenic
NM_002449.5(MSX2):c.265_266delinsTA (p.Ala89Ter)	indel	Parietal foramina 1 [RCV000018478]	Chr5:174724924..174724925 [GRCh38] Chr5:174151927..174151928 [GRCh37] Chr5:5q35.2	pathogenic
NM_002449.5(MSX2):c.345del (p.Ala114_Trp115insTer)	deletion	Parietal foramina 1 [RCV000018479]	Chr5:174725003 [GRCh38] Chr5:174152006 [GRCh37] Chr5:5q35.2	pathogenic
NM_002449.5(MSX2):c.505_508dup (p.Ala170fs)	duplication	Parietal foramina with cleidocranial dysplasia [RCV000018480]	Chr5:174729283..174729284 [GRCh38] Chr5:174156286..174156287 [GRCh37] Chr5:5q35.2	pathogenic
NM_002449.5(MSX2):c.548_555del (p.Glu183fs)	deletion	Parietal foramina 1 [RCV000018481]	Chr5:174729324..174729331 [GRCh38] Chr5:174156327..174156334 [GRCh37] Chr5:5q35.2	pathogenic
GRCh38/hg38 5q32-35.3(chr5:149714592-181272151)x3	copy number gain	See cases [RCV000051863]	Chr5:149714592..181272151 [GRCh38] Chr5:149094155..180699152 [GRCh37] Chr5:149074348..180631758 [NCBI36] Chr5:5q32-35.3	pathogenic
GRCh38/hg38 5q33.3-35.3(chr5:160029980-181269805)x3	copy number gain	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051865]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051865]\|See cases [RCV000051865]	Chr5:160029980..181269805 [GRCh38] Chr5:159456987..180696806 [GRCh37] Chr5:159389565..180629412 [NCBI36] Chr5:5q33.3-35.3	pathogenic
GRCh38/hg38 5q34-35.3(chr5:168689326-181269946)x3	copy number gain	See cases [RCV000051866]	Chr5:168689326..181269946 [GRCh38] Chr5:168116331..180696947 [GRCh37] Chr5:168048909..180629553 [NCBI36] Chr5:5q34-35.3	pathogenic
GRCh38/hg38 5q35.1-35.2(chr5:172961091-175054665)x1	copy number loss	See cases [RCV000052150]	Chr5:172961091..175054665 [GRCh38] Chr5:172388094..174481668 [GRCh37] Chr5:172320700..174414274 [NCBI36] Chr5:5q35.1-35.2	pathogenic
GRCh38/hg38 5q33.3-35.3(chr5:156825512-181269805)x3	copy number gain	See cases [RCV000133847]	Chr5:156825512..181269805 [GRCh38] Chr5:156252523..180696806 [GRCh37] Chr5:156185101..180629412 [NCBI36] Chr5:5q33.3-35.3	pathogenic
GRCh38/hg38 5q35.2(chr5:173949773-174900395)x1	copy number loss	See cases [RCV000135638]	Chr5:173949773..174900395 [GRCh38] Chr5:173376776..174327398 [GRCh37] Chr5:173309382..174260004 [NCBI36] Chr5:5q35.2	pathogenic
GRCh38/hg38 5q34-35.3(chr5:164386701-181269805)x3	copy number gain	See cases [RCV000135546]	Chr5:164386701..181269805 [GRCh38] Chr5:163813707..180696806 [GRCh37] Chr5:163746285..180629412 [NCBI36] Chr5:5q34-35.3	pathogenic
GRCh38/hg38 5q35.1-35.3(chr5:169334755-181285301)x3	copy number gain	See cases [RCV000141249]	Chr5:169334755..181285301 [GRCh38] Chr5:168761759..180712302 [GRCh37] Chr5:168694337..180644908 [NCBI36] Chr5:5q35.1-35.3	pathogenic
GRCh38/hg38 5q35.1-35.2(chr5:173237772-176614618)x3	copy number gain	See cases [RCV000142647]	Chr5:173237772..176614618 [GRCh38] Chr5:172664775..176041619 [GRCh37] Chr5:172597381..175974225 [NCBI36] Chr5:5q35.1-35.2	pathogenic
GRCh38/hg38 5q35.2(chr5:174724141-174742787)x1	copy number loss	See cases [RCV000143339]	Chr5:174724141..174742787 [GRCh38] Chr5:174151144..174169790 [GRCh37] Chr5:174083750..174102396 [NCBI36] Chr5:5q35.2	pathogenic
NM_002449.5(MSX2):c.-42C>T	single nucleotide variant	Craniosynostosis 2 [RCV000264746]\|Parietal foramina 1 [RCV000359264]	Chr5:174724618 [GRCh38] Chr5:174151621 [GRCh37] Chr5:5q35.2	benign\|likely benign\|uncertain significance
NM_002449.5(MSX2):c.*363A>G	single nucleotide variant	Craniosynostosis 2 [RCV000260056]\|Parietal foramina 1 [RCV000375711]	Chr5:174729946 [GRCh38] Chr5:174156949 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.375G>T (p.Pro125=)	single nucleotide variant	not specified [RCV000194886]	Chr5:174725034 [GRCh38] Chr5:174152037 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.443C>T (p.Pro148Leu)	single nucleotide variant	Craniosynostosis 2 [RCV000203576]\|Enlarged parietal foramina [RCV000690192]	Chr5:174729222 [GRCh38] Chr5:174156225 [GRCh37] Chr5:5q35.2	pathogenic\|likely pathogenic
GRCh37/hg19 5q35.2(chr5:173043321-174953690)x3	copy number gain	Ductal breast carcinoma [RCV000207114]	Chr5:173043321..174953690 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.360C>T (p.Gly120=)	single nucleotide variant	Parietal foramina 1 [RCV000525101]	Chr5:174725019 [GRCh38] Chr5:174152022 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.386T>C (p.Met129Thr)	single nucleotide variant	Craniosynostosis 2 [RCV000270658]\|Enlarged parietal foramina [RCV001513220]\|Parietal foramina 1 [RCV000987635]\|not provided [RCV001711690]\|not specified [RCV000246108]	Chr5:174729165 [GRCh38] Chr5:174156168 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*510A>G	single nucleotide variant	Craniosynostosis 2 [RCV000286620]\|Parietal foramina 1 [RCV000339309]	Chr5:174730093 [GRCh38] Chr5:174157096 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*1125A>G	single nucleotide variant	Craniosynostosis 2 [RCV000280532]\|Parietal foramina 1 [RCV000337904]	Chr5:174730708 [GRCh38] Chr5:174157711 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*46G>T	single nucleotide variant	Craniosynostosis 2 [RCV000337817]\|Parietal foramina 1 [RCV000280472]	Chr5:174729629 [GRCh38] Chr5:174156632 [GRCh37] Chr5:5q35.2	likely benign\|uncertain significance
NM_002449.5(MSX2):c.*349T>C	single nucleotide variant	Craniosynostosis 2 [RCV000275136]\|Parietal foramina 1 [RCV000318732]	Chr5:174729932 [GRCh38] Chr5:174156935 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.635C>G (p.Ala212Gly)	single nucleotide variant	Craniosynostosis 2 [RCV000276654]\|Parietal foramina 1 [RCV000389679]	Chr5:174729414 [GRCh38] Chr5:174156417 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*723A>C	single nucleotide variant	Craniosynostosis 2 [RCV000353287]\|Parietal foramina 1 [RCV000300717]	Chr5:174730306 [GRCh38] Chr5:174157309 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*416A>C	single nucleotide variant	Craniosynostosis 2 [RCV000317572]\|Parietal foramina 1 [RCV000378679]	Chr5:174729999 [GRCh38] Chr5:174157002 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*1249T>C	single nucleotide variant	Craniosynostosis 2 [RCV000359784]\|Parietal foramina 1 [RCV000302601]	Chr5:174730832 [GRCh38] Chr5:174157835 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*172G>A	single nucleotide variant	Craniosynostosis 2 [RCV000346807]\|Parietal foramina 1 [RCV000303826]	Chr5:174729755 [GRCh38] Chr5:174156758 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*1007T>A	single nucleotide variant	Craniosynostosis 2 [RCV000288160]\|Parietal foramina 1 [RCV000326904]	Chr5:174730590 [GRCh38] Chr5:174157593 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*526T>C	single nucleotide variant	Craniosynostosis 2 [RCV000289882]\|Parietal foramina 1 [RCV000377617]	Chr5:174730109 [GRCh38] Chr5:174157112 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.-50C>T	single nucleotide variant	Craniosynostosis 2 [RCV000304545]\|Parietal foramina 1 [RCV000393390]	Chr5:174724610 [GRCh38] Chr5:174151613 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*1176G>C	single nucleotide variant	Craniosynostosis 2 [RCV000359850]\|Parietal foramina 1 [RCV000393366]	Chr5:174730759 [GRCh38] Chr5:174157762 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*257T>C	single nucleotide variant	Craniosynostosis 2 [RCV000397493]\|Parietal foramina 1 [RCV000307215]	Chr5:174729840 [GRCh38] Chr5:174156843 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*144C>T	single nucleotide variant	Craniosynostosis 2 [RCV000343515]\|Parietal foramina 1 [RCV000405689]	Chr5:174729727 [GRCh38] Chr5:174156730 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.-17C>G	single nucleotide variant	Craniosynostosis 2 [RCV000365140]\|Parietal foramina 1 [RCV000310571]\|not provided [RCV001653694]	Chr5:174724643 [GRCh38] Chr5:174151646 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*1006dup	duplication	Craniosynostosis syndrome [RCV000327898]\|Enlarged parietal foramina [RCV000384938]	Chr5:174730580..174730581 [GRCh38] Chr5:174157583..174157584 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*658C>T	single nucleotide variant	Craniosynostosis 2 [RCV000396378]\|Parietal foramina 1 [RCV000368464]	Chr5:174730241 [GRCh38] Chr5:174157244 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*647C>T	single nucleotide variant	Craniosynostosis 2 [RCV000404786]\|Parietal foramina 1 [RCV000311469]	Chr5:174730230 [GRCh38] Chr5:174157233 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*1096A>G	single nucleotide variant	Craniosynostosis 2 [RCV000349154]\|Parietal foramina 1 [RCV000406371]	Chr5:174730679 [GRCh38] Chr5:174157682 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*1146T>C	single nucleotide variant	Craniosynostosis 2 [RCV000403211]\|Parietal foramina 1 [RCV000298013]	Chr5:174730729 [GRCh38] Chr5:174157732 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.699G>A (p.Ala233=)	single nucleotide variant	Craniosynostosis 2 [RCV000331763]\|Parietal foramina 1 [RCV000542377]	Chr5:174729478 [GRCh38] Chr5:174156481 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*1312A>G	single nucleotide variant	Craniosynostosis 2 [RCV000272150]\|Parietal foramina 1 [RCV000329321]	Chr5:174730895 [GRCh38] Chr5:174157898 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*863A>G	single nucleotide variant	Craniosynostosis 2 [RCV000260811]\|Parietal foramina 1 [RCV000324500]	Chr5:174730446 [GRCh38] Chr5:174157449 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*289A>G	single nucleotide variant	Craniosynostosis 2 [RCV000364259]\|Parietal foramina 1 [RCV000276383]	Chr5:174729872 [GRCh38] Chr5:174156875 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*946T>G	single nucleotide variant	Craniosynostosis 2 [RCV000358161]\|Parietal foramina 1 [RCV000265716]	Chr5:174730529 [GRCh38] Chr5:174157532 [GRCh37] Chr5:5q35.2	uncertain significance
GRCh37/hg19 5q15-35.3(chr5:94844077-178830410)x3	copy number gain	not provided [RCV000487658]	Chr5:94844077..178830410 [GRCh37] Chr5:5q15-35.3	likely benign
NM_002449.5(MSX2):c.*306G>T	single nucleotide variant	Craniosynostosis 2 [RCV000367369]\|Parietal foramina 1 [RCV000315104]	Chr5:174729889 [GRCh38] Chr5:174156892 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*530A>G	single nucleotide variant	Craniosynostosis 2 [RCV000403936]\|Parietal foramina 1 [RCV000347144]	Chr5:174730113 [GRCh38] Chr5:174157116 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*102C>T	single nucleotide variant	Craniosynostosis 2 [RCV000286224]\|Parietal foramina 1 [RCV000371419]	Chr5:174729685 [GRCh38] Chr5:174156688 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*1086dup	duplication	Craniosynostosis syndrome [RCV000388421]\|Enlarged parietal foramina [RCV000296539]	Chr5:174730663..174730664 [GRCh38] Chr5:174157666..174157667 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.*601C>T	single nucleotide variant	Craniosynostosis 2 [RCV000288658]\|Parietal foramina 1 [RCV000351073]	Chr5:174730184 [GRCh38] Chr5:174157187 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*512G>T	single nucleotide variant	Craniosynostosis 2 [RCV001151927]\|Parietal foramina 1 [RCV001151928]	Chr5:174730095 [GRCh38] Chr5:174157098 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.514C>G (p.Arg172Gly)	single nucleotide variant	not provided [RCV000585463]	Chr5:174729293 [GRCh38] Chr5:174156296 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*1050T>C	single nucleotide variant	Craniosynostosis 2 [RCV001152033]\|Parietal foramina 1 [RCV001152032]	Chr5:174730633 [GRCh38] Chr5:174157636 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*157A>T	single nucleotide variant	Craniosynostosis 2 [RCV001151846]\|Parietal foramina 1 [RCV001151845]	Chr5:174729740 [GRCh38] Chr5:174156743 [GRCh37] Chr5:5q35.2	benign
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789)	copy number gain	See cases [RCV000510723]	Chr5:113577..180719789 [GRCh37] Chr5:5p15.33-q35.3	pathogenic
GRCh37/hg19 5q21.3-35.3(chr5:106716357-180687338)x3	copy number gain	See cases [RCV000448245]	Chr5:106716357..180687338 [GRCh37] Chr5:5q21.3-35.3	pathogenic
GRCh37/hg19 5q35.1-35.3(chr5:171396359-180719789)x3	copy number gain	See cases [RCV000448458]	Chr5:171396359..180719789 [GRCh37] Chr5:5q35.1-35.3	pathogenic
GRCh37/hg19 5q35.1-35.3(chr5:172031248-180719789)x3	copy number gain	See cases [RCV000512068]	Chr5:172031248..180719789 [GRCh37] Chr5:5q35.1-35.3	pathogenic
GRCh37/hg19 5p15.1-q35.2(chr5:17628741-176575720)x1	copy number loss	See cases [RCV000511978]	Chr5:17628741..176575720 [GRCh37] Chr5:5p15.1-q35.2	pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789)x3	copy number gain	See cases [RCV000512039]	Chr5:113577..180719789 [GRCh37] Chr5:5p15.33-q35.3	pathogenic
NM_002449.5(MSX2):c.698C>T (p.Ala233Val)	single nucleotide variant	Enlarged parietal foramina [RCV000644909]	Chr5:174729477 [GRCh38] Chr5:174156480 [GRCh37] Chr5:5q35.2	uncertain significance
GRCh37/hg19 5q35.2(chr5:174070065-174601039)x3	copy number gain	not provided [RCV000682613]	Chr5:174070065..174601039 [GRCh37] Chr5:5q35.2	uncertain significance
GRCh37/hg19 5p15.33-q35.3(chr5:25328-180693344)x3	copy number gain	not provided [RCV000744323]	Chr5:25328..180693344 [GRCh37] Chr5:5p15.33-q35.3	pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:13648-180905029)x3	copy number gain	not provided [RCV000744317]	Chr5:13648..180905029 [GRCh37] Chr5:5p15.33-q35.3	pathogenic
GRCh37/hg19 5q33.2-35.3(chr5:155344802-180693344)x3	copy number gain	not provided [RCV000745284]	Chr5:155344802..180693344 [GRCh37] Chr5:5q33.2-35.3	pathogenic
GRCh37/hg19 5q35.2(chr5:174130513-174193309)x3	copy number gain	not provided [RCV000745334]	Chr5:174130513..174193309 [GRCh37] Chr5:5q35.2	benign
Single allele	duplication	not provided [RCV001691163]	Chr5:174724439..174724440 [GRCh38] Chr5:174151442..174151443 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.379+68C>T	single nucleotide variant	not provided [RCV001708748]	Chr5:174725106 [GRCh38] Chr5:174152109 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.803A>G (p.Ter268=)	single nucleotide variant	Enlarged parietal foramina [RCV001478215]\|not provided [RCV000938412]	Chr5:174729582 [GRCh38] Chr5:174156585 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.723G>A (p.Pro241=)	single nucleotide variant	Enlarged parietal foramina [RCV002064508]\|not provided [RCV000864904]	Chr5:174729502 [GRCh38] Chr5:174156505 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.442C>T (p.Pro148Ser)	single nucleotide variant	Enlarged parietal foramina [RCV000792855]	Chr5:174729221 [GRCh38] Chr5:174156224 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.255C>T (p.Gly85=)	single nucleotide variant	Enlarged parietal foramina [RCV000804878]	Chr5:174724914 [GRCh38] Chr5:174151917 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.380-9G>C	single nucleotide variant	not provided [RCV000960701]	Chr5:174729150 [GRCh38] Chr5:174156153 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.-56C>A	single nucleotide variant	Craniosynostosis 2 [RCV001151732]\|Parietal foramina 1 [RCV001151733]	Chr5:174724604 [GRCh38] Chr5:174151607 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*106C>T	single nucleotide variant	Craniosynostosis 2 [RCV001151842]\|Parietal foramina 1 [RCV001151841]	Chr5:174729689 [GRCh38] Chr5:174156692 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.380-164G>A	single nucleotide variant	Parietal foramina 1 [RCV000987634]\|not provided [RCV001619870]	Chr5:174728995 [GRCh38] Chr5:174155998 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*1178C>T	single nucleotide variant	Craniosynostosis 2 [RCV001155903]\|Parietal foramina 1 [RCV001155904]	Chr5:174730761 [GRCh38] Chr5:174157764 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*878C>T	single nucleotide variant	Craniosynostosis 2 [RCV001157504]\|Parietal foramina 1 [RCV001157503]	Chr5:174730461 [GRCh38] Chr5:174157464 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*1206T>C	single nucleotide variant	Craniosynostosis 2 [RCV001157606]\|Parietal foramina 1 [RCV001157607]	Chr5:174730789 [GRCh38] Chr5:174157792 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*1233T>C	single nucleotide variant	Craniosynostosis 2 [RCV001157608]\|Parietal foramina 1 [RCV001157609]	Chr5:174730816 [GRCh38] Chr5:174157819 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.793C>T (p.His265Tyr)	single nucleotide variant	Craniosynostosis 2 [RCV001197937]	Chr5:174729572 [GRCh38] Chr5:174156575 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.315G>C (p.Lys105Asn)	single nucleotide variant	Craniosynostosis 2 [RCV001155621]\|Parietal foramina 1 [RCV001155622]	Chr5:174724974 [GRCh38] Chr5:174151977 [GRCh37] Chr5:5q35.2	benign\|likely benign
NM_002449.5(MSX2):c.*366T>G	single nucleotide variant	Craniosynostosis 2 [RCV001155703]\|Parietal foramina 1 [RCV001155704]	Chr5:174729949 [GRCh38] Chr5:174156952 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.380-305C>T	single nucleotide variant	not provided [RCV001570988]	Chr5:174728854 [GRCh38] Chr5:174155857 [GRCh37] Chr5:5q35.2	likely benign
Single allele	duplication	not provided [RCV001650693]	Chr5:174724413..174724414 [GRCh38] Chr5:174151416..174151417 [GRCh37] Chr5:5q35.2	benign
Single allele	duplication	not provided [RCV001720942]	Chr5:174724439..174724440 [GRCh38] Chr5:174151442..174151443 [GRCh37] Chr5:5q35.2	benign
Single allele	deletion	not provided [RCV001615520]	Chr5:174724414 [GRCh38] Chr5:174151417 [GRCh37] Chr5:5q35.2	benign
Single allele	duplication	not provided [RCV001679978]	Chr5:174724413..174724414 [GRCh38] Chr5:174151416..174151417 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.379+59G>A	single nucleotide variant	not provided [RCV001641999]	Chr5:174725097 [GRCh38] Chr5:174152100 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.380-166G>A	single nucleotide variant	not provided [RCV001586471]	Chr5:174728993 [GRCh38] Chr5:174155996 [GRCh37] Chr5:5q35.2	likely benign
Single allele	duplication	not provided [RCV001718106]	Chr5:174724413..174724414 [GRCh38] Chr5:174151416..174151417 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.379+274G>A	single nucleotide variant	not provided [RCV001594173]	Chr5:174725312 [GRCh38] Chr5:174152315 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.380-162A>G	single nucleotide variant	not provided [RCV001557933]	Chr5:174728997 [GRCh38] Chr5:174156000 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.*465C>T	single nucleotide variant	Craniosynostosis 2 [RCV001157396]\|Parietal foramina 1 [RCV001157397]	Chr5:174730048 [GRCh38] Chr5:174157051 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.495G>A (p.Gln165=)	single nucleotide variant	not provided [RCV000913863]	Chr5:174729274 [GRCh38] Chr5:174156277 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.380-191TG[13]	microsatellite	not provided [RCV001570428]	Chr5:174728968..174728969 [GRCh38] Chr5:174155971..174155972 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.379+69C>T	single nucleotide variant	not provided [RCV001654951]	Chr5:174725107 [GRCh38] Chr5:174152110 [GRCh37] Chr5:5q35.2	benign
Single allele	deletion	not provided [RCV001608504]	Chr5:174724439 [GRCh38] Chr5:174151442 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.380-191TG[11]	microsatellite	not provided [RCV001598911]	Chr5:174728968..174728973 [GRCh38] Chr5:174155971..174155976 [GRCh37] Chr5:5q35.2	benign
Single allele	insertion	not provided [RCV001638487]	Chr5:174724412..174724413 [GRCh38] Chr5:174151415..174151416 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*644C>T	single nucleotide variant	Craniosynostosis 2 [RCV001155801]\|Parietal foramina 1 [RCV001155800]	Chr5:174730227 [GRCh38] Chr5:174157230 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.751C>T (p.Pro251Ser)	single nucleotide variant	Craniosynostosis 2 [RCV001157290]\|Parietal foramina 1 [RCV001157289]	Chr5:174729530 [GRCh38] Chr5:174156533 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*466G>A	single nucleotide variant	Craniosynostosis 2 [RCV001157399]\|Parietal foramina 1 [RCV001157398]	Chr5:174730049 [GRCh38] Chr5:174157052 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*126T>C	single nucleotide variant	Craniosynostosis 2 [RCV001151844]\|Parietal foramina 1 [RCV001151843]	Chr5:174729709 [GRCh38] Chr5:174156712 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*516A>G	single nucleotide variant	Craniosynostosis 2 [RCV001151930]\|Parietal foramina 1 [RCV001151929]	Chr5:174730099 [GRCh38] Chr5:174157102 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.122A>T (p.Lys41Met)	single nucleotide variant	Craniosynostosis 2 [RCV001152972]\|Parietal foramina 1 [RCV001152973]	Chr5:174724781 [GRCh38] Chr5:174151784 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.286G>T (p.Val96Leu)	single nucleotide variant	Craniosynostosis 2 [RCV001152974]\|Enlarged parietal foramina [RCV002032410]\|Parietal foramina 1 [RCV001152975]\|not specified [RCV001819860]	Chr5:174724945 [GRCh38] Chr5:174151948 [GRCh37] Chr5:5q35.2	likely benign\|uncertain significance
NM_002449.5(MSX2):c.*183G>T	single nucleotide variant	Craniosynostosis 2 [RCV001153087]\|Parietal foramina 1 [RCV001153086]	Chr5:174729766 [GRCh38] Chr5:174156769 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*635G>A	single nucleotide variant	Craniosynostosis 2 [RCV001153195]\|Parietal foramina 1 [RCV001153194]	Chr5:174730218 [GRCh38] Chr5:174157221 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*601C>G	single nucleotide variant	Craniosynostosis 2 [RCV001153192]\|Parietal foramina 1 [RCV001153193]	Chr5:174730184 [GRCh38] Chr5:174157187 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*1064A>G	single nucleotide variant	Craniosynostosis 2 [RCV001152034]\|Parietal foramina 1 [RCV001152035]	Chr5:174730647 [GRCh38] Chr5:174157650 [GRCh37] Chr5:5q35.2	uncertain significance
Single allele	deletion	not provided [RCV001669205]	Chr5:174724414..174724415 [GRCh38] Chr5:174151417..174151418 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.380-160_380-159del	microsatellite	not provided [RCV001685873]	Chr5:174728996..174728997 [GRCh38] Chr5:174155999..174156000 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.380-163TA[3]	microsatellite	not provided [RCV001685577]	Chr5:174728995..174728996 [GRCh38] Chr5:174155998..174155999 [GRCh37] Chr5:5q35.2	benign
Single allele	single nucleotide variant	not provided [RCV001682385]	Chr5:174724413 [GRCh38] Chr5:174151416 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.*1189G>A	single nucleotide variant	Craniosynostosis 2 [RCV001155905]\|Parietal foramina 1 [RCV001155906]	Chr5:174730772 [GRCh38] Chr5:174157775 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.304G>A (p.Ala102Thr)	single nucleotide variant	Craniosynostosis 2 [RCV001152977]\|Parietal foramina 1 [RCV001152976]	Chr5:174724963 [GRCh38] Chr5:174151966 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.*1161C>T	single nucleotide variant	Craniosynostosis 2 [RCV001153306]\|Parietal foramina 1 [RCV001153305]	Chr5:174730744 [GRCh38] Chr5:174157747 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.698dup (p.Ser234fs)	duplication	Craniosynostosis 2 [RCV001197187]	Chr5:174729476..174729477 [GRCh38] Chr5:174156479..174156480 [GRCh37] Chr5:5q35.2	uncertain significance
GRCh37/hg19 5q35.2(chr5:173830823-174344055)x3	copy number gain	not provided [RCV001259929]	Chr5:173830823..174344055 [GRCh37] Chr5:5q35.2	uncertain significance
GRCh37/hg19 5q35.1-35.3(chr5:170805664-180719789)x3	copy number gain	5q35 microduplication syndrome [RCV001263227]	Chr5:170805664..180719789 [GRCh37] Chr5:5q35.1-35.3	pathogenic
NM_002449.5(MSX2):c.745A>G (p.Ile249Val)	single nucleotide variant	Enlarged parietal foramina [RCV001298842]	Chr5:174729524 [GRCh38] Chr5:174156527 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.572A>G (p.Gln191Arg)	single nucleotide variant	not provided [RCV001357858]	Chr5:174729351 [GRCh38] Chr5:174156354 [GRCh37] Chr5:5q35.2	uncertain significance
Single allele	single nucleotide variant	not provided [RCV001534295]	Chr5:174724464 [GRCh38] Chr5:174151467 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.380-191TG[12]	microsatellite	not provided [RCV001614979]	Chr5:174728968..174728971 [GRCh38] Chr5:174155971..174155974 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.380-48T>A	single nucleotide variant	not provided [RCV001537102]	Chr5:174729111 [GRCh38] Chr5:174156114 [GRCh37] Chr5:5q35.2	benign
Single allele	duplication	not provided [RCV001616145]	Chr5:174724439..174724440 [GRCh38] Chr5:174151442..174151443 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.379+8C>G	single nucleotide variant	Enlarged parietal foramina [RCV001428105]	Chr5:174725046 [GRCh38] Chr5:174152049 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.577C>T (p.Arg193Ter)	single nucleotide variant	not provided [RCV001727343]	Chr5:174729356 [GRCh38] Chr5:174156359 [GRCh37] Chr5:5q35.2	likely pathogenic
NM_002449.5(MSX2):c.380-191TG[9]	microsatellite	not provided [RCV001776508]	Chr5:174728968..174728977 [GRCh38] Chr5:174155971..174155980 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.749C>T (p.Pro250Leu)	single nucleotide variant	Enlarged parietal foramina [RCV001971581]	Chr5:174729528 [GRCh38] Chr5:174156531 [GRCh37] Chr5:5q35.2	uncertain significance
GRCh37/hg19 5q35.2(chr5:174147094-174200503)x1	copy number loss	not provided [RCV001827833]	Chr5:174147094..174200503 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.457C>T (p.Gln153Ter)	single nucleotide variant	Enlarged parietal foramina [RCV001949945]	Chr5:174729236 [GRCh38] Chr5:174156239 [GRCh37] Chr5:5q35.2	pathogenic
NM_002449.5(MSX2):c.484C>T (p.Arg162Cys)	single nucleotide variant	Enlarged parietal foramina [RCV001895407]	Chr5:174729263 [GRCh38] Chr5:174156266 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.77C>T (p.Pro26Leu)	single nucleotide variant	Enlarged parietal foramina [RCV001863829]	Chr5:174724736 [GRCh38] Chr5:174151739 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.505A>G (p.Ile169Val)	single nucleotide variant	Enlarged parietal foramina [RCV001874279]	Chr5:174729284 [GRCh38] Chr5:174156287 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.152C>T (p.Ala51Val)	single nucleotide variant	Enlarged parietal foramina [RCV001912364]	Chr5:174724811 [GRCh38] Chr5:174151814 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.143G>C (p.Ser48Thr)	single nucleotide variant	Enlarged parietal foramina [RCV001912092]	Chr5:174724802 [GRCh38] Chr5:174151805 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.95A>T (p.Glu32Val)	single nucleotide variant	Enlarged parietal foramina [RCV001993595]	Chr5:174724754 [GRCh38] Chr5:174151757 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.178A>C (p.Lys60Gln)	single nucleotide variant	Enlarged parietal foramina [RCV001992775]	Chr5:174724837 [GRCh38] Chr5:174151840 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.428G>A (p.Arg143Gln)	single nucleotide variant	Enlarged parietal foramina [RCV001996470]	Chr5:174729207 [GRCh38] Chr5:174156210 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.449C>G (p.Thr150Ser)	single nucleotide variant	Enlarged parietal foramina [RCV001878775]	Chr5:174729228 [GRCh38] Chr5:174156231 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.179A>C (p.Lys60Thr)	single nucleotide variant	Enlarged parietal foramina [RCV001876607]	Chr5:174724838 [GRCh38] Chr5:174151841 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.83C>T (p.Pro28Leu)	single nucleotide variant	Enlarged parietal foramina [RCV001898133]	Chr5:174724742 [GRCh38] Chr5:174151745 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.712G>A (p.Ala238Thr)	single nucleotide variant	Enlarged parietal foramina [RCV001957221]	Chr5:174729491 [GRCh38] Chr5:174156494 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.22A>C (p.Asn8His)	single nucleotide variant	Enlarged parietal foramina [RCV001993685]	Chr5:174724681 [GRCh38] Chr5:174151684 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.103G>C (p.Ala35Pro)	single nucleotide variant	not provided [RCV002224853]	Chr5:174724762 [GRCh38] Chr5:174151765 [GRCh37] Chr5:5q35.2	uncertain significance
NM_002449.5(MSX2):c.49G>A (p.Gly17Ser)	single nucleotide variant	Enlarged parietal foramina [RCV002206890]	Chr5:174724708 [GRCh38] Chr5:174151711 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.174G>A (p.Pro58=)	single nucleotide variant	Enlarged parietal foramina [RCV002191774]	Chr5:174724833 [GRCh38] Chr5:174151836 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.750G>A (p.Pro250=)	single nucleotide variant	Enlarged parietal foramina [RCV002152508]	Chr5:174729529 [GRCh38] Chr5:174156532 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.252C>T (p.His84=)	single nucleotide variant	Enlarged parietal foramina [RCV002079754]	Chr5:174724911 [GRCh38] Chr5:174151914 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.380-18C>G	single nucleotide variant	Enlarged parietal foramina [RCV002196298]	Chr5:174729141 [GRCh38] Chr5:174156144 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.228G>A (p.Leu76=)	single nucleotide variant	Enlarged parietal foramina [RCV002079048]	Chr5:174724887 [GRCh38] Chr5:174151890 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.117C>T (p.Arg39=)	single nucleotide variant	Enlarged parietal foramina [RCV002151737]	Chr5:174724776 [GRCh38] Chr5:174151779 [GRCh37] Chr5:5q35.2	benign
NM_002449.5(MSX2):c.379+7G>C	single nucleotide variant	Enlarged parietal foramina [RCV002079845]	Chr5:174725045 [GRCh38] Chr5:174152048 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.379+9G>A	single nucleotide variant	Enlarged parietal foramina [RCV002103663]	Chr5:174725047 [GRCh38] Chr5:174152050 [GRCh37] Chr5:5q35.2	likely benign
NM_002449.5(MSX2):c.756G>A (p.Val252=)	single nucleotide variant	Enlarged parietal foramina [RCV002216838]	Chr5:174729535 [GRCh38] Chr5:174156538 [GRCh37] Chr5:5q35.2	benign

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:7392	AgrOrtholog
COSMIC	MSX2	COSMIC
Ensembl Genes	ENSG00000120149	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSP00000239243	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSP00000427425	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENST00000239243	ENTREZGENE, UniProtKB/Swiss-Prot
	ENST00000507785	ENTREZGENE, UniProtKB/TrEMBL
GTEx	ENSG00000120149	GTEx
HGNC ID	HGNC:7392	ENTREZGENE
Human Proteome Map	MSX2	Human Proteome Map
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot
	Homeobox_CS	UniProtKB/Swiss-Prot
	Homeobox_dom	UniProtKB/Swiss-Prot
	Homeobox_metazoa	UniProtKB/Swiss-Prot
KEGG Report	hsa:4488	UniProtKB/Swiss-Prot
NCBI Gene	4488	ENTREZGENE
OMIM	123101	OMIM
	168500	OMIM
	168550	OMIM
	604757	OMIM
Pfam	Homeodomain	UniProtKB/Swiss-Prot
PharmGKB	PA31197	PharmGKB
PRINTS	HOMEOBOX	UniProtKB/Swiss-Prot
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot
	HOMEOBOX_2	UniProtKB/Swiss-Prot
SMART	HOX	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot
UniProt	D6RIS4_HUMAN	UniProtKB/TrEMBL
	MSX2_HUMAN	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	D3DQN1	UniProtKB/Swiss-Prot
	Q53XM4	UniProtKB/Swiss-Prot
	Q9UD60	UniProtKB/Swiss-Prot

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MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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