PHF5A (PHD finger protein 5A) - Rat Genome Database

Name: PHF5A
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: PHF5A (PHD finger protein 5A) Homo sapiens

Analyze

Symbol:

PHF5A

Name:

PHD finger protein 5A

RGD ID:

1348043

HGNC Page

HGNC:18000

Description:

Enables RNA binding activity and zinc ion binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of U12-type spliceosomal complex; U2 snRNP; and U2-type precatalytic spliceosome.

Type:

protein-coding

RefSeq Status:

REVIEWED

Previously known as:

bK223H9.2; INI; MGC1346; PHD finger-like domain protein 5A; PHD finger-like domain-containing protein 5A; PHD-finger 5a; Rds3; SAP14b; SF3b14b; SF3B7; splicing factor 3B associated 14 kDa protein; splicing factor 3b, subunit 7; splicing factor 3B-associated 14 kDa protein

RGD Orthologs

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):	Phf5a (PHD finger protein 5A)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Rattus norvegicus (Norway rat):	Phf5a (PHD finger protein 5A)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Chinchilla lanigera (long-tailed chinchilla):	Phf5a (PHD finger protein 5A)	NCBI	Ortholog
Pan paniscus (bonobo/pygmy chimpanzee):	PHF5A (PHD finger protein 5A)	NCBI	Ortholog
Canis lupus familiaris (dog):	PHF5A (PHD finger protein 5A)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Phf5a (PHD finger protein 5A)	NCBI	Ortholog
Sus scrofa (pig):	PHF5A (PHD finger protein 5A)	HGNC	Ensembl, NCBI, OrthoDB
Chlorocebus sabaeus (green monkey):	PHF5A (PHD finger protein 5A)	NCBI	Ortholog
Heterocephalus glaber (naked mole-rat):	Phf5a (PHD finger protein 5A)	NCBI	Ortholog
Alliance orthologs ³
Rattus norvegicus (Norway rat):	Phf5a (PHD finger protein 5A)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Phf5a (PHD finger protein 5A)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	phf5a (PHD finger protein 5A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid\|ZFIN)
Saccharomyces cerevisiae (baker's yeast):	RDS3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Phf5a	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	phf-5	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus laevis (African clawed frog):	phf5a.S	Alliance	DIOPT (Xenbase)
Xenopus tropicalis (tropical clawed frog):	phf5a	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Xenopus laevis (African clawed frog):	phf5a.L	Alliance	DIOPT (Xenbase)

Related Pseudogenes:

PHF5AP1 PHF5AP2 PHF5AP3 PHF5AP4 PHF5AP5 PHF5AP6 PHF5AP7

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	22	41,459,717 - 41,468,692 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	22	41,459,717 - 41,468,692 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	22	41,855,721 - 41,864,696 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	22	40,185,667 - 40,194,654 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	22	40,180,221 - 40,189,208	NCBI
Celera	22	25,662,105 - 25,671,092 (-)	NCBI		Celera
Cytogenetic Map	22	q13.2	NCBI
HuRef	22	24,821,678 - 24,830,510 (-)	NCBI		HuRef
CHM1_1	22	41,815,604 - 41,824,591 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	22	41,938,569 - 41,947,547 (-)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

adenylosuccinase lyase deficiency (IAGP)

common variable immunodeficiency 4 (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2,4,6-trinitrotoluene (ISO)

2,6-dinitrotoluene (ISO)

2-hydroxypropanoic acid (EXP)

3-isobutyl-1-methyl-7H-xanthine (EXP)

4,4'-sulfonyldiphenol (EXP)

aflatoxin B1 (ISO)

amiodarone (EXP)

arsenous acid (EXP)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (EXP)

bisphenol A (EXP,ISO)

butanal (EXP)

cadmium dichloride (EXP)

chlorpyrifos (ISO)

clobetasol (ISO)

crocidolite asbestos (EXP)

dexamethasone (EXP)

diarsenic trioxide (EXP)

enzyme inhibitor (EXP)

ethanol (EXP)

fenthion (ISO)

fipronil (ISO)

flavonoids (ISO)

flutamide (ISO)

folic acid (EXP,ISO)

FR900359 (EXP)

gentamycin (ISO)

indometacin (EXP)

ivermectin (EXP)

lead(0) (EXP)

nefazodone (ISO)

nimesulide (ISO)

paracetamol (ISO)

phenol red (EXP)

picoxystrobin (EXP)

rac-lactic acid (EXP)

resveratrol (EXP,ISO)

rotenone (ISO)

silicon dioxide (EXP)

tamoxifen (ISO)

tetrachloromethane (ISO)

toluene (ISO)

trichostatin A (EXP)

trimellitic anhydride (ISO)

Triptolide (ISO)

triptonide (ISO)

tungsten (ISO)

tunicamycin (EXP)

valproic acid (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

mRNA processing (IEA)

mRNA splicing, via spliceosome (IBA,IDA,IEA,NAS)

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

RNA splicing (IEA)

stem cell differentiation (IEA)

U2-type prespliceosome assembly (NAS)

Cellular Component

nuclear matrix (IEA)

nuclear speck (IEA,ISS)

nucleolus (ISO)

nucleoplasm (IDA,TAS)

nucleus (IDA,IEA,NAS)

precatalytic spliceosome (IBA)

spliceosomal complex (IEA,NAS)

U12-type spliceosomal complex (IBA,IDA)

U2 snRNP (IBA,IDA,NAS)

U2-type precatalytic spliceosome (IDA)

U2-type spliceosomal complex (IDA,IPI)

Molecular Function

DNA binding (IEA)

metal ion binding (IEA)

protein binding (IPI,ISO)

RNA binding (HDA,IDA,IEA)

zinc ion binding (IDA)

Molecular Pathway Annotations Click to see Annotation Detail View

spliceosome pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
2.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:10591208	PMID:12054543	PMID:12226669	PMID:12234937	PMID:12477932	PMID:15146077	PMID:15461802	PMID:15489334	PMID:17332742	PMID:18076038	PMID:19394292	PMID:20360068
PMID:21873635	PMID:21988832	PMID:22365833	PMID:22658674	PMID:22681889	PMID:22939629	PMID:23602568	PMID:23651857	PMID:24457600	PMID:24705354	PMID:24981860	PMID:25963833
PMID:26244496	PMID:26344197	PMID:26496610	PMID:26527279	PMID:27634302	PMID:27684187	PMID:27720643	PMID:28077445	PMID:28330616	PMID:28541300	PMID:28561026	PMID:29128334
PMID:29298432	PMID:29360106	PMID:29566713	PMID:29700004	PMID:29802200	PMID:29845934	PMID:30033366	PMID:30404004	PMID:30463901	PMID:30572598	PMID:30766880	PMID:30804502
PMID:30890647	PMID:30932358	PMID:30948266	PMID:31054974	PMID:31076518	PMID:31091453	PMID:31182584	PMID:31363146	PMID:31744343	PMID:31753913	PMID:31980649	PMID:32129710
PMID:32228507	PMID:32416067	PMID:32494006	PMID:32694731	PMID:32698014	PMID:32707033	PMID:32780723	PMID:32807901	PMID:32814053	PMID:32989298	PMID:33226137	PMID:33277362
PMID:33301849	PMID:33306668	PMID:33545068	PMID:33938017	PMID:33961781	PMID:34133714	PMID:34373451	PMID:34597346	PMID:34672954	PMID:34709727	PMID:34822310	PMID:35013218
PMID:35271311	PMID:35559673	PMID:35777798	PMID:35831314	PMID:35906200	PMID:35941108	PMID:35944360	PMID:36244648	PMID:36373674	PMID:36537216	PMID:36581580	PMID:36792075
PMID:36797247	PMID:37422718	PMID:37434235	PMID:37499664	PMID:37845358	PMID:37866880	PMID:38113892	PMID:38429756

Genomics

Comparative Map Data

PHF5A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	22	41,459,717 - 41,468,692 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	22	41,459,717 - 41,468,692 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	22	41,855,721 - 41,864,696 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	22	40,185,667 - 40,194,654 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	22	40,180,221 - 40,189,208	NCBI
Celera	22	25,662,105 - 25,671,092 (-)	NCBI		Celera
Cytogenetic Map	22	q13.2	NCBI
HuRef	22	24,821,678 - 24,830,510 (-)	NCBI		HuRef
CHM1_1	22	41,815,604 - 41,824,591 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	22	41,938,569 - 41,947,547 (-)	NCBI		T2T-CHM13v2.0

Phf5a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	81,748,717 - 81,756,093 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	15	81,748,721 - 81,756,112 (-)	Ensembl		GRCm39 Ensembl
GRCm38	15	81,864,516 - 81,871,892 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	81,864,520 - 81,871,911 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	81,694,946 - 81,702,322 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	15	81,692,572 - 81,699,158 (-)	NCBI		MGSCv36	mm8
Celera	15	83,983,598 - 83,990,971 (-)	NCBI		Celera
Cytogenetic Map	15	E1	NCBI
cM Map	15	38.26	NCBI

Phf5a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	115,258,609 - 115,265,174 (-)	NCBI		GRCr8
mRatBN7.2	7	113,378,469 - 113,385,035 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	113,378,471 - 113,385,460 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	115,140,892 - 115,147,461 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	117,364,388 - 117,370,956 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	117,333,828 - 117,340,397 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	123,095,286 - 123,101,851 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	123,095,288 - 123,101,869 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	123,070,681 - 123,077,246 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	120,216,581 - 120,223,146 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	7	120,250,812 - 120,257,376 (-)	NCBI
Celera	7	109,697,147 - 109,703,712 (-)	NCBI		Celera
Cytogenetic Map	7	q34	NCBI

Phf5a
(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	NW_004955413	27,018,730 - 27,026,937 (-)	NCBI	ChiLan1.0	ChiLan1.0

PHF5A
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	23	51,290,050 - 51,299,113 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	22	53,989,315 - 53,998,375 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	22	22,353,811 - 22,362,899 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	22	40,441,275 - 40,450,174 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	22	40,441,275 - 40,450,174 (-)	Ensembl	panpan1.1		panPan2

PHF5A
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	10	23,798,854 - 23,809,024 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	23,798,969 - 23,808,865 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	23,731,535 - 23,741,497 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	24,543,712 - 24,553,684 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	24,543,361 - 24,554,077 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	24,260,490 - 24,270,455 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	24,581,379 - 24,591,328 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	24,755,822 - 24,765,792 (+)	NCBI		UU_Cfam_GSD_1.0

Phf5a
(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_024404945	7,442,447 - 7,451,501 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936492	452,628 - 461,910 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936492	452,628 - 461,915 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PHF5A
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	7,071,484 - 7,081,407 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	7,071,145 - 7,080,046 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PHF5A
(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	19	23,998,277 - 24,008,504 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	19	23,998,127 - 24,008,173 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	101,410,244 - 101,420,144 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Phf5a
(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_female_1.0 Ensembl	NW_004624752	7,114,274 - 7,123,706 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624752	7,114,239 - 7,123,706 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in PHF5A
2 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 22q12.3-13.33(chr22:33768441-50739977)x3	copy number gain	See cases [RCV000051682]	Chr22:33768441..50739977 [GRCh38] Chr22:34164428..51178405 [GRCh37] Chr22:32494428..49525271 [NCBI36] Chr22:22q12.3-13.33	pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:37061769-50738932)x3	copy number gain	See cases [RCV000051684]	Chr22:37061769..50738932 [GRCh38] Chr22:37457809..51177360 [GRCh37] Chr22:35787755..49524226 [NCBI36] Chr22:22q12.3-13.33	pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3	copy number gain	See cases [RCV000133646]	Chr22:16916608..50739836 [GRCh38] Chr22:17397498..51178264 [GRCh37] Chr22:15777498..49525130 [NCBI36] Chr22:22q11.1-13.33	pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3	copy number gain	See cases [RCV000134730]	Chr22:16916743..50739785 [GRCh38] Chr22:17397633..51178213 [GRCh37] Chr22:15777633..49525079 [NCBI36] Chr22:22q11.1-13.33	pathogenic
GRCh38/hg38 22q13.1-13.33(chr22:40202014-50735806)x3	copy number gain	See cases [RCV000134513]	Chr22:40202014..50735806 [GRCh38] Chr22:40598018..51174234 [GRCh37] Chr22:38927964..49521100 [NCBI36] Chr22:22q13.1-13.33	pathogenic
GRCh38/hg38 22q13.2(chr22:41277822-42414957)x3	copy number gain	See cases [RCV000136785]	Chr22:41277822..42414957 [GRCh38] Chr22:41673826..42810963 [GRCh37] Chr22:40003772..41140907 [NCBI36] Chr22:22q13.2	pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237518)x3	copy number gain	See cases [RCV000240091]	Chr22:16054691..51237518 [GRCh37] Chr22:22q11.1-13.33	pathogenic
GRCh37/hg19 22q12.3-13.33(chr22:35728929-51220961)x3	copy number gain	See cases [RCV000240469]	Chr22:35728929..51220961 [GRCh37] Chr22:22q12.3-13.33	pathogenic
GRCh37/hg19 22q13.1-13.33(chr22:40425714-51220961)x3	copy number gain	See cases [RCV000240459]	Chr22:40425714..51220961 [GRCh37] Chr22:22q13.1-13.33	pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51220902)x3	copy number gain	See cases [RCV000446956]	Chr22:16054691..51220902 [GRCh37] Chr22:22q11.1-13.33	pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237463)x3	copy number gain	See cases [RCV000448847]	Chr22:16054691..51237463 [GRCh37] Chr22:22q11.1-13.33	pathogenic
GRCh37/hg19 22q13.2(chr22:41835094-42756616)x3	copy number gain	See cases [RCV000511241]	Chr22:41835094..42756616 [GRCh37] Chr22:22q13.2	uncertain significance
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838)	copy number gain	See cases [RCV000510873]	Chr22:16888900..51197838 [GRCh37] Chr22:22q11.1-13.33	pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838)x3	copy number gain	See cases [RCV000512333]	Chr22:16888900..51197838 [GRCh37] Chr22:22q11.1-13.33	pathogenic
NC_000022.11:g.(?_41301335)_(42070317_?)del	deletion	Immunodeficiency, common variable, 4 [RCV000648330]	Chr22:41301335..42070317 [GRCh38] Chr22:41697339..42466321 [GRCh37] Chr22:22q13.2	uncertain significance
GRCh37/hg19 22q13.2(chr22:41849322-42756616)x3	copy number gain	not provided [RCV000684486]	Chr22:41849322..42756616 [GRCh37] Chr22:22q13.2	likely pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054667-51243435)x3	copy number gain	not provided [RCV000741689]	Chr22:16054667..51243435 [GRCh37] Chr22:22q11.1-13.33	pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51195728)x3	copy number gain	not provided [RCV000741691]	Chr22:16114244..51195728 [GRCh37] Chr22:22q11.1-13.33	pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51211392)x3	copy number gain	not provided [RCV000741692]	Chr22:16114244..51211392 [GRCh37] Chr22:22q11.1-13.33	pathogenic
GRCh37/hg19 22q12.2-13.33(chr22:30654764-51197838)x3	copy number gain	not provided [RCV001007181]	Chr22:30654764..51197838 [GRCh37] Chr22:22q12.2-13.33	pathogenic
GRCh37/hg19 22q13.2(chr22:41742988-41946225)x3	copy number gain	not provided [RCV000848205]	Chr22:41742988..41946225 [GRCh37] Chr22:22q13.2	uncertain significance
GRCh37/hg19 22q11.1-13.33(chr22:16888899-51197838)x3	copy number gain	not provided [RCV000846344]	Chr22:16888899..51197838 [GRCh37] Chr22:22q11.1-13.33	pathogenic
GRCh37/hg19 22q13.1-13.33(chr22:40502364-51197838)x3	copy number gain	not provided [RCV001007502]	Chr22:40502364..51197838 [GRCh37] Chr22:22q13.1-13.33	pathogenic
GRCh37/hg19 22q13.2(chr22:41853620-42385978)x1	copy number loss	not provided [RCV001258783]	Chr22:41853620..42385978 [GRCh37] Chr22:22q13.2	uncertain significance
GRCh37/hg19 22q11.1-13.33(chr22:16197005-51224252)x3	copy number gain	See cases [RCV001263056]	Chr22:16197005..51224252 [GRCh37] Chr22:22q11.1-13.33	pathogenic
NC_000022.10:g.(?_41697339)_(42466321_?)del	deletion	Common variable immunodeficiency 4 [RCV001305750]	Chr22:41697339..42466321 [GRCh37] Chr22:22q13.2	uncertain significance
NM_032758.4(PHF5A):c.11A>G (p.His4Arg)	single nucleotide variant	not provided [RCV001733301]	Chr22:41468643 [GRCh38] Chr22:41864647 [GRCh37] Chr22:22q13.2	uncertain significance
GRCh37/hg19 22q13.2(chr22:41742988-41946225)x3	copy number gain	not provided [RCV001825236]	Chr22:41742988..41946225 [GRCh37] Chr22:22q13.2	not provided
NC_000022.10:g.(?_41277754)_(43089957_?)dup	duplication	Immunodeficiency, common variable, 4 [RCV001979926]	Chr22:41277754..43089957 [GRCh37] Chr22:22q13.2	uncertain significance
NC_000022.10:g.(?_35776672)_(42486826_?)dup	duplication	Adenylosuccinate lyase deficiency [RCV003119093]	Chr22:35776672..42486826 [GRCh37] Chr22:22q12.3-13.2	uncertain significance
GRCh37/hg19 22q13.1-13.2(chr22:39768795-41946225)x3	copy number gain	not provided [RCV002475709]	Chr22:39768795..41946225 [GRCh37] Chr22:22q13.1-13.2	uncertain significance
NM_032758.4(PHF5A):c.110_111del (p.Val37fs)	microsatellite	not provided [RCV003387645]	Chr22:41467580..41467581 [GRCh38] Chr22:41863584..41863585 [GRCh37] Chr22:22q13.2	uncertain significance
GRCh37/hg19 22q13.1-13.2(chr22:40545592-42096995)x3	copy number gain	Syndromic craniosynostosis [RCV003481509]	Chr22:40545592..42096995 [GRCh37] Chr22:22q13.1-13.2	likely pathogenic
NM_032758.4(PHF5A):c.77G>T (p.Cys26Phe)	single nucleotide variant	not provided [RCV003437617]	Chr22:41467614 [GRCh38] Chr22:41863618 [GRCh37] Chr22:22q13.2	uncertain significance
GRCh37/hg19 22q13.1-13.31(chr22:39044105-45794212)x3	copy number gain	not specified [RCV003986179]	Chr22:39044105..45794212 [GRCh37] Chr22:22q13.1-13.31	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	882
Count of miRNA genes:	565
Interacting mature miRNAs:	625
Transcripts:	ENST00000216252, ENST00000459687, ENST00000491254
Prediction methods:	Miranda, Rnahybrid, Targetscan
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

adipose tissue

appendage

entire extraembryonic component

High

Medium

2431

2412

1684

586

1616

428

4351

2010

3395

404

1448

1607

171

1204

2784

Low

572

332

183

313

Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_032758	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AL008582	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC007321	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC075808	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BK000563	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BU584712	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH471095	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068256	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CR456398	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KT584885	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000216252 ⟹ ENSP00000216252

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	41,459,717 - 41,468,692 (-)	Ensembl

RefSeq Acc Id:

ENST00000459687

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	41,460,303 - 41,468,625 (-)	Ensembl

RefSeq Acc Id:

ENST00000491254

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	22	41,460,432 - 41,468,499 (-)	Ensembl

RefSeq Acc Id:

NM_032758 ⟹ NP_116147

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	22	41,459,717 - 41,468,692 (-)	NCBI
GRCh37	22	41,855,721 - 41,864,708 (-)	RGD
Build 36	22	40,185,667 - 40,194,654 (-)	NCBI Archive
Celera	22	25,662,105 - 25,671,092 (-)	RGD
HuRef	22	24,821,678 - 24,830,510 (-)	RGD
CHM1_1	22	41,815,604 - 41,824,591 (-)	NCBI
T2T-CHM13v2.0	22	41,938,569 - 41,947,547 (-)	NCBI

Sequence:

show sequence

AGTTCCCGAAGCTTCCGGTGGCCGGCTTAGTTAGGAGCTATGGCTAAACATCATCCTGATTTGA
TCTTTTGCCGCAAGCAGGCTGGTGTTGCCATCGGAAGACTGTGTGAAAAATGTGATGGCAAGTG
TGTGATTTGTGACTCCTATGTGCGTCCCTGCACTCTGGTGCGCATATGTGATGAGTGTAACTAT
GGATCTTACCAGGGGCGCTGTGTGATCTGTGGAGGACCTGGGGTCTCTGATGCCTATTATTGTA
AGGAGTGCACCATCCAGGAGAAGGACAGAGATGGCTGCCCAAAGATTGTCAATCTGGGGAGCTC
TAAGACAGACCTCTTCTATGAACGCAAAAAATACGGCTTCAAGAAGAGGTGATTGGTGGGTGGC
CCCTTCCTCCCCCCAACATCAGTCTGCTGCAGCTGCCAGAAAACATGCCTACTACTACCAGCAG
AAAGGGAGCAGAGCCCAGAGCATCACCAGGAGTGCCTGCTAGTGTACTGGCAGCTTGCCACCCC
CTCCTCTCCCTTCACCCAGACACGTGGTAGGGATGGAAAAGGATTCTTCACAGAGCACTCTGGC
ACACCATATCGGAGAAAACTTGATAGATTAGTTAATGGTTTTTCTTGAATTCGAGAAGCAAAGA
TCTGTTCTCCATATTGGTATGTTCTCCCTCAACCAAGATCTTCTAAAAAGAAATAATATTTTAG
TCTTCTGCTTGAGGAACTGACTGTGAAGCGACGCCCAGTGAAAAACATGTTCTTGCAGCAGCTC
TGGTGGCAGCTGTCCTTGAGGAACCTTTGGTGTGTGGTGGGAAGCTATCAGAACAAGAAATGTA
GGCATTTCCCGTTTTTTTTGGGGGGGGGGTGGGGGGGCAGGGCTCTGCCCTCTTGAAAGGCATT
TACTTGTTTAACACTTGTCCAGCTACAGTGGGGTACAGTAGCTGGCTATTCACAGGCATCATCA
TAGCCCACTAGTCTCATATTATTTTCCTTTTGAGAAATTGGAAACTCTTTCTGTTGCTATTATA
TTAATAAAGTTGGTGTTTATTTTCTGGTA

hide sequence

Protein Sequences


Protein RefSeqs	NP_116147	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH07321	(Get FASTA)	NCBI Sequence Viewer
	AAH75808	(Get FASTA)	NCBI Sequence Viewer
	CAG30284	(Get FASTA)	NCBI Sequence Viewer
	DAA00074	(Get FASTA)	NCBI Sequence Viewer
	EAW60433	(Get FASTA)	NCBI Sequence Viewer
	EAW60434	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSP00000216252
	ENSP00000216252.3
GenBank Protein	Q7RTV0	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_116147 ⟸ NM_032758
- UniProtKB:	Q9UH06 (UniProtKB/Swiss-Prot), Q7RTV0 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGP GVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR hide sequence

RefSeq Acc Id:

ENSP00000216252 ⟸ ENST00000216252

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q7RTV0-F1-model_v2	AlphaFold	Q7RTV0	1-110	view protein structure

Promoters

RGD ID:

6799654

Promoter ID:

HG_KWN:42986

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

CD4+TCell, CD4+TCell_12Hour, CD4+TCell_2Hour, HeLa_S3, Jurkat, K562, Lymphoblastoid, NB4

Transcripts:

NM_001098, OTTHUMT00000259153, OTTHUMT00000320686, OTTHUMT00000320687, OTTHUMT00000320688, UC003BAD.1

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	22	40,193,851 - 40,195,152 (+)	MPROMDB

RGD ID:

13604258

Promoter ID:

EPDNEW_H28313

Type:

initiation region

Name:

PHF5A_1

Description:

PHD finger protein 5A

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	22	41,468,678 - 41,468,738	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:18000	AgrOrtholog
COSMIC	PHF5A	COSMIC
Ensembl Genes	ENSG00000100410	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENST00000216252	ENTREZGENE
	ENST00000216252.4	UniProtKB/Swiss-Prot
GTEx	ENSG00000100410	GTEx
HGNC ID	HGNC:18000	ENTREZGENE
Human Proteome Map	PHF5A	Human Proteome Map
InterPro	PHF5	UniProtKB/Swiss-Prot
KEGG Report	hsa:84844	UniProtKB/Swiss-Prot
NCBI Gene	84844	ENTREZGENE
OMIM	617846	OMIM
PANTHER	PHD FINGER-LIKE DOMAIN-CONTAINING PROTEIN 5A	UniProtKB/Swiss-Prot
	PTHR13120	UniProtKB/Swiss-Prot
Pfam	PHF5	UniProtKB/Swiss-Prot
PharmGKB	PA134876104	PharmGKB
PIRSF	PHF5	UniProtKB/Swiss-Prot
UniProt	PHF5A_HUMAN	UniProtKB/Swiss-Prot, ENTREZGENE
	Q9UH06	ENTREZGENE
UniProt Secondary	Q9UH06	UniProtKB/Swiss-Prot

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

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

Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)

Send us a Message

Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)