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Gene: ALX1 (ALX homeobox 1) Homo sapiens

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Symbol:

ALX1

Name:

ALX homeobox 1

RGD ID:

732877

HGNC Page

HGNC:1494

Description:

Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in positive regulation of epithelial to mesenchymal transition and positive regulation of transcription by RNA polymerase II. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Located in Golgi apparatus and nuclear body. Implicated in frontonasal dysplasia 3.

Type:

protein-coding

RefSeq Status:

REVIEWED

Previously known as:

ALX homeobox protein 1; CART-1; CART1; cartilage paired-class homeoprotein 1; epididymis luminal protein 23; FND3; HEL23

RGD Orthologs

Alliance Orthologs

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):	Alx1 (ALX homeobox 1)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Rattus norvegicus (Norway rat):	Alx1 (ALX homeobox 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Pan paniscus (bonobo/pygmy chimpanzee):	ALX1 (ALX homeobox 1)	NCBI	Ortholog
Canis lupus familiaris (dog):	ALX1 (ALX homeobox 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, PhylomeDB, Treefam
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Alx1 (ALX homeobox 1)	NCBI	Ortholog
Sus scrofa (pig):	ALX1 (ALX homeobox 1)	HGNC	Ensembl, Inparanoid, NCBI, OrthoDB
Chlorocebus sabaeus (green monkey):	ALX1 (ALX homeobox 1)	NCBI	Ortholog
Alliance orthologs ³
Rattus norvegicus (Norway rat):	Alx1 (ALX homeobox 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Alx1 (ALX homeobox 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	alx1 (ALX homeobox 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid\|ZFIN)
Drosophila melanogaster (fruit fly):	Pph13	Alliance	DIOPT (PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	dsc-1	Alliance	DIOPT (InParanoid\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	alx1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoInspector\|PANTHER\|PhylomeDB)
Xenopus laevis (African clawed frog):	alx1.L	Alliance	DIOPT (Xenbase)
Xenopus laevis (African clawed frog):	alx1.S	Alliance	DIOPT (Xenbase)

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	12	85,280,220 - 85,301,784 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	85,280,220 - 85,301,784 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	85,673,998 - 85,695,562 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	84,198,167 - 84,219,693 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	84,176,352 - 84,198,027	NCBI
Celera	12	85,337,491 - 85,358,941 (+)	NCBI		Celera
Cytogenetic Map	12	q21.31	NCBI
HuRef	12	82,731,405 - 82,752,155 (+)	NCBI		HuRef
CHM1_1	12	85,638,988 - 85,660,512 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	85,260,566 - 85,282,129 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	anencephaly		ISO	Alx1 (Mus musculus)	734689		RGD

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	frontonasal dysplasia 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Frontonasal dysplasia 3	ClinVar	PMID:20451171
ALX1	Human	frontonasal dysplasia 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: ALX1-related condition	ClinVar	PMID:24467814 more ...
ALX1	Human	frontonasal dysplasia 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: ALX1-related condition	ClinVar	PMID:28492532
ALX1	Human	frontonasal dysplasia 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Frontonasal dysplasia 3	ClinVar	PMID:25741868
ALX1	Human	frontonasal dysplasia 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: ALX1-related condition	ClinVar	PMID:25741868 and PMID:28492532
ALX1	Human	frontonasal dysplasia 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Frontonasal dysplasia 3	ClinVar
ALX1	Human	frontonasal dysplasia 3		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Frontonasal dysplasia 3	ClinVar	PMID:27324866
ALX1	Human	genetic disease		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Inborn genetic diseases	ClinVar	PMID:28492532
ALX1	Human	genetic disease		IAGP	(Homo sapiens) more ...	8554872	ClinVar Annotator: match by term: Inborn genetic diseases	ClinVar
ALX1	Human	lung adenocarcinoma		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Lung adenocarcinoma	ClinVar	PMID:27993330

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	Craniofacial Abnormalities		EXP		11554173	CTD Direct Evidence: marker/mechanism	CTD	PMID:9847249
ALX1	Human	frontonasal dysplasia		EXP		11554173	CTD Direct Evidence: marker/mechanism	CTD

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	frontonasal dysplasia 3		ISS	Alx1 (Mus musculus)	13592920	OMIM:613456	MouseDO

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	frontonasal dysplasia 3		IAGP		7240710		OMIM

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	(+)-catechin	multiple interactions	EXP		6480464	[Catechin co-treated with Grape Seed Proanthocyanidins] results in decreased expression of ALX1 mRNA	CTD	PMID:24763279
ALX1	Human	2,3,7,8-tetrachlorodibenzodioxine	affects expression	ISO	Alx1 (Mus musculus)	6480464	Tetrachlorodibenzodioxin affects the expression of ALX1 mRNA	CTD	PMID:24058054
ALX1	Human	2,3,7,8-tetrachlorodibenzodioxine	increases expression	ISO	Alx1 (Rattus norvegicus)	6480464	Tetrachlorodibenzodioxin results in increased expression of ALX1 mRNA	CTD	PMID:33387578
ALX1	Human	2,3,7,8-tetrachlorodibenzodioxine	decreases expression	ISO	Alx1 (Mus musculus)	6480464	Tetrachlorodibenzodioxin results in decreased expression of ALX1 mRNA	CTD	PMID:37854252
ALX1	Human	2,3,7,8-tetrachlorodibenzodioxine	decreases expression	ISO	Alx1 (Rattus norvegicus)	6480464	Tetrachlorodibenzodioxin results in decreased expression of ALX1 mRNA	CTD	PMID:11752688
ALX1	Human	3,3',5,5'-tetrabromobisphenol A	increases expression	ISO	Alx1 (Mus musculus)	6480464	tetrabromobisphenol A results in increased expression of ALX1 mRNA	CTD	PMID:25172293
ALX1	Human	4,4'-sulfonyldiphenol	increases expression	ISO	Alx1 (Mus musculus)	6480464	bisphenol S results in increased expression of ALX1 mRNA	CTD	PMID:30951980
ALX1	Human	acetaldehyde	affects expression	ISO	Alx1 (Mus musculus)	6480464	Acetaldehyde affects the expression of ALX1 mRNA	CTD	PMID:22634333
ALX1	Human	aflatoxin B1	decreases methylation	EXP		6480464	Aflatoxin B1 results in decreased methylation of ALX1 gene	CTD	PMID:27153756
ALX1	Human	all-trans-retinoic acid	increases expression	EXP		6480464	Tretinoin results in increased expression of ALX1 mRNA	CTD	PMID:21934132
ALX1	Human	ammonium chloride	affects expression	ISO	Alx1 (Rattus norvegicus)	6480464	Ammonium Chloride affects the expression of ALX1 mRNA	CTD	PMID:16483693
ALX1	Human	benzo[a]pyrene	decreases expression	ISO	Alx1 (Rattus norvegicus)	6480464	Benzo(a)pyrene results in decreased expression of ALX1 mRNA	CTD	PMID:21839799
ALX1	Human	benzo[a]pyrene	affects methylation	EXP		6480464	Benzo(a)pyrene affects the methylation of ALX1 promoter	CTD	PMID:27901495
ALX1	Human	bis(2-ethylhexyl) phthalate	increases expression	ISO	Alx1 (Mus musculus)	6480464	Diethylhexyl Phthalate results in increased expression of ALX1 mRNA	CTD	PMID:34319233
ALX1	Human	bisphenol A	decreases expression	ISO	Alx1 (Rattus norvegicus)	6480464	bisphenol A results in decreased expression of ALX1 mRNA	CTD	PMID:25181051 and PMID:34947998
ALX1	Human	bisphenol A	increases expression	ISO	Alx1 (Mus musculus)	6480464	bisphenol A results in increased expression of ALX1 mRNA	CTD	PMID:30951980
ALX1	Human	bisphenol A	increases methylation	ISO	Alx1 (Mus musculus)	6480464	bisphenol A results in increased methylation of ALX1 promoter	CTD	PMID:27312807
ALX1	Human	bisphenol F	increases expression	ISO	Alx1 (Mus musculus)	6480464	bisphenol F results in increased expression of ALX1 mRNA	CTD	PMID:30951980
ALX1	Human	casticin	decreases expression	ISO	Alx1 (Mus musculus)	6480464	casticin results in decreased expression of ALX1 mRNA	CTD	PMID:28444820
ALX1	Human	copper atom	increases expression	ISO	Alx1 (Rattus norvegicus)	6480464	Copper deficiency results in increased expression of ALX1 mRNA	CTD	PMID:26033743
ALX1	Human	copper atom	multiple interactions	ISO	Alx1 (Rattus norvegicus)	6480464	[Copper co-treated with Dietary Sucrose] results in increased expression of ALX1 mRNA	CTD	PMID:26033743
ALX1	Human	copper(0)	increases expression	ISO	Alx1 (Rattus norvegicus)	6480464	Copper deficiency results in increased expression of ALX1 mRNA	CTD	PMID:26033743
ALX1	Human	copper(0)	multiple interactions	ISO	Alx1 (Rattus norvegicus)	6480464	[Copper co-treated with Dietary Sucrose] results in increased expression of ALX1 mRNA	CTD	PMID:26033743
ALX1	Human	diquat	decreases expression	ISO	Alx1 (Mus musculus)	6480464	Diquat results in decreased expression of ALX1 mRNA	CTD	PMID:36851058
ALX1	Human	dorsomorphin	multiple interactions	EXP		6480464	[NOG protein co-treated with Panobinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1 more ...	CTD	PMID:27188386
ALX1	Human	flusilazole	increases expression	ISO	Alx1 (Rattus norvegicus)	6480464	flusilazole results in increased expression of ALX1 mRNA	CTD	PMID:28263823
ALX1	Human	lipopolysaccharide	multiple interactions	EXP		6480464	[S-(1 and 2-dichlorovinyl)cysteine affects the susceptibility to Lipopolysaccharides] which results in increased expression of ALX1 mRNA	CTD	PMID:35811015
ALX1	Human	panobinostat	increases expression	EXP		6480464	panobinostat results in increased expression of ALX1 mRNA	CTD	PMID:26272509
ALX1	Human	panobinostat	multiple interactions	EXP		6480464	[NOG protein co-treated with Panobinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1 and 3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of ALX1 mRNA	CTD	PMID:27188386
ALX1	Human	paracetamol	decreases expression	EXP		6480464	Acetaminophen results in decreased expression of ALX1 mRNA	CTD	PMID:26690555
ALX1	Human	phenylmercury acetate	increases expression	EXP		6480464	Phenylmercuric Acetate results in increased expression of ALX1 mRNA	CTD	PMID:26272509
ALX1	Human	phenylmercury acetate	multiple interactions	EXP		6480464	[NOG protein co-treated with Phenylmercuric Acetate co-treated with dorsomorphin co-treated with 4-(5-benzo(1 and 3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of ALX1 mRNA	CTD	PMID:27188386
ALX1	Human	S-(1,2-dichlorovinyl)-L-cysteine	multiple interactions	EXP		6480464	[S-(1 and 2-dichlorovinyl)cysteine affects the susceptibility to Lipopolysaccharides] which results in increased expression of ALX1 mRNA	CTD	PMID:35811015
ALX1	Human	SB 431542	multiple interactions	EXP		6480464	[NOG protein co-treated with Panobinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1 more ...	CTD	PMID:27188386
ALX1	Human	sodium arsenite	increases expression	EXP		6480464	sodium arsenite results in increased expression of ALX1 mRNA	CTD	PMID:22714537
ALX1	Human	temozolomide	decreases expression	EXP		6480464	Temozolomide results in decreased expression of ALX1 mRNA	CTD	PMID:31758290
ALX1	Human	titanium dioxide	decreases methylation	ISO	Alx1 (Mus musculus)	6480464	titanium dioxide results in decreased methylation of ALX1 gene	CTD	PMID:35295148
ALX1	Human	titanium dioxide	increases methylation	EXP		6480464	titanium dioxide results in increased methylation of ALX1 gene	CTD	PMID:34973136
ALX1	Human	trichloroethene	increases expression	ISO	Alx1 (Rattus norvegicus)	6480464	Trichloroethylene results in increased expression of ALX1 mRNA	CTD	PMID:33387578
ALX1	Human	trichostatin A	increases expression	EXP		6480464	trichostatin A results in increased expression of ALX1 mRNA	CTD	PMID:24935251 and PMID:26272509
ALX1	Human	trichostatin A	multiple interactions	EXP		6480464	[NOG protein co-treated with trichostatin A co-treated with dorsomorphin co-treated with 4-(5-benzo(1 and 3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of ALX1 mRNA	CTD	PMID:27188386
ALX1	Human	valproic acid	affects expression	EXP		6480464	Valproic Acid affects the expression of ALX1 mRNA	CTD	PMID:25979313
ALX1	Human	valproic acid	increases expression	EXP		6480464	Valproic Acid results in increased expression of ALX1 mRNA	CTD	PMID:23179753 more ...
ALX1	Human	valproic acid	multiple interactions	EXP		6480464	[NOG protein co-treated with Valproic Acid co-treated with dorsomorphin co-treated with 4-(5-benzo(1 and 3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of ALX1 mRNA	CTD	PMID:27188386
ALX1	Human	vorinostat	multiple interactions	EXP		6480464	[NOG protein co-treated with Vorinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1 and 3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of ALX1 mRNA	CTD	PMID:27188386
ALX1	Human	vorinostat	increases expression	EXP		6480464	vorinostat results in increased expression of ALX1 mRNA	CTD	PMID:26272509

Biological Process

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	anterior/posterior pattern specification	acts_upstream_of_or_within	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	embryonic limb morphogenesis	acts_upstream_of_or_within	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	embryonic skeletal system morphogenesis	involved_in	IBA	MGI:104621 more ...	150520179		GO_Central	GO_REF:0000033
ALX1	Human	embryonic skeletal system morphogenesis	acts_upstream_of_or_within	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	mesenchymal cell development	acts_upstream_of_or_within	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	negative regulation of DNA-templated transcription	involved_in	IBA	PANTHER:PTN002803087 more ...	150520179		GO_Central	GO_REF:0000033
ALX1	Human	negative regulation of transcription by RNA polymerase II	acts_upstream_of_or_within	IDA		150520179	PMID:8756334	MGI	PMID:8756334
ALX1	Human	neural tube closure	acts_upstream_of_or_within	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	positive regulation of DNA-templated transcription	involved_in	IDA		150520179	PMID:9753625	UniProt	PMID:9753625
ALX1	Human	positive regulation of DNA-templated transcription	involved_in	IMP		150520179	PMID:23288509	UniProt	PMID:23288509
ALX1	Human	positive regulation of epithelial to mesenchymal transition	involved_in	IMP		150520179	PMID:23288509	UniProt	PMID:23288509
ALX1	Human	positive regulation of transcription by RNA polymerase II	involved_in	IDA		150520179	PMID:9753625	NTNU_SB	PMID:9753625
ALX1	Human	positive regulation of transcription by RNA polymerase II	acts_upstream_of_or_within	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	positive regulation of transcription by RNA polymerase II	involved_in	IBA	MGI:104621 more ...	150520179		GO_Central	GO_REF:0000033
ALX1	Human	regulation of DNA-templated transcription	involved_in	IEA	InterPro:IPR017970	150520179		InterPro	GO_REF:0000002
ALX1	Human	roof of mouth development	acts_upstream_of_or_within	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	stem cell development	acts_upstream_of_or_within	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107

Cellular Component

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	chromatin	located_in	ISA	tfclass:3.1.3	150520179		NTNU_SB	GO_REF:0000113
ALX1	Human	Golgi apparatus	located_in	IDA		150520179		HPA	GO_REF:0000052
ALX1	Human	nuclear body	located_in	IDA		150520179		HPA	GO_REF:0000052
ALX1	Human	nucleoplasm	located_in	IDA		150520179		HPA	GO_REF:0000052
ALX1	Human	nucleus	located_in	IEA	UniProtKB-SubCell:SL-0191	150520179		UniProt	GO_REF:0000044
ALX1	Human	nucleus	located_in	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	nucleus	located_in	IEA	UniProtKB-KW:KW-0539	150520179		UniProt	GO_REF:0000043
ALX1	Human	nucleus	located_in	IEA	UniRule:UR000401037	150520179		UniProt	GO_REF:0000104
ALX1	Human	nucleus	located_in	IDA		150520179	PMID:23288509 and PMID:9753625	UniProt	PMID:23288509 and PMID:9753625
ALX1	Human	transcription regulator complex	part_of	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107

Molecular Function

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	DNA binding	NOT\|enables	ISO	Alx1 (Rattus norvegicus)	9068941	PMID:12390248	UniProt	PMID:12390248 and REF_RGD_ID:10047318
ALX1	Human	DNA binding	enables	IEA	UniProtKB-KW:KW-0238 and UniProtKB-KW:KW-0371	150520179		UniProt	GO_REF:0000043
ALX1	Human	DNA binding	enables	IEA	InterPro:IPR001356	150520179		InterPro	GO_REF:0000002
ALX1	Human	DNA binding	enables	IEA	UniRule:UR000401037	150520179		UniProt	GO_REF:0000104
ALX1	Human	DNA-binding transcription activator activity, RNA polymerase II-specific	enables	TAS		150520179	PMID:8756334	GO_Central	PMID:8756334
ALX1	Human	DNA-binding transcription activator activity, RNA polymerase II-specific	enables	IBA	PANTHER:PTN002803087 and UniProtKB:Q15699	150520179		GO_Central	GO_REF:0000033
ALX1	Human	DNA-binding transcription activator activity, RNA polymerase II-specific	enables	IDA		150520179	PMID:9753625	NTNU_SB	PMID:9753625
ALX1	Human	DNA-binding transcription factor activity		ISO	Alx1 (Rattus norvegicus)	9068941		RGD	PMID:12929931 and REF_RGD_ID:1358475
ALX1	Human	DNA-binding transcription factor activity	enables	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	DNA-binding transcription factor activity, RNA polymerase II-specific	enables	ISA	tfclass:3.1.3	150520179		NTNU_SB	GO_REF:0000113
ALX1	Human	DNA-binding transcription factor activity, RNA polymerase II-specific	enables	IEA	InterPro:IPR017970	150520179		InterPro	GO_REF:0000002
ALX1	Human	protein binding	enables	IPI	UniProtKB:O94829	150520179	PMID:16189514	IntAct	PMID:16189514
ALX1	Human	protein binding	enables	IPI	UniProtKB:O95833 more ...	150520179	PMID:32296183	IntAct	PMID:32296183
ALX1	Human	protein homodimerization activity	enables	ISO	Alx1 (Rattus norvegicus)	9068941	PMID:12390248	UniProt	PMID:12390248 and REF_RGD_ID:10047318
ALX1	Human	RNA polymerase II transcription regulatory region sequence-specific DNA binding	enables	IBA	FB:FBgn0011701 more ...	150520179		GO_Central	GO_REF:0000033
ALX1	Human	RNA polymerase II transcription regulatory region sequence-specific DNA binding	enables	IDA		150520179	PMID:9753625	NTNU_SB	PMID:9753625
ALX1	Human	sequence-specific DNA binding	enables	IEA	UniProtKB:Q8C8B0 and ensembl:ENSMUSP00000129230	150520179		Ensembl	GO_REF:0000107
ALX1	Human	sequence-specific double-stranded DNA binding	enables	IDA		150520179	PMID:28473536	ARUK-UCL	PMID:28473536
ALX1	Human	sequence-specific double-stranded DNA binding	enables	IEA	ARBA:ARBA00028376	150520179		UniProt	GO_REF:0000117

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	Absent eyebrow		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Agenesis of corpus callosum		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Aplasia/Hypoplasia of the frontal sinuses		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Autosomal recessive inheritance		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Bifid nose		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Brachycephaly		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Brachydactyly		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Camptodactyly of finger		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Cataract		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Cleft palate		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Cleft palate		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Conductive hearing impairment		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Cranium bifidum occultum		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Epicanthus		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Eyelid coloboma		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Finger clinodactyly		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Hypertelorism		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Hypertelorism		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Hypoplasia of the frontal bone		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Hypoplasia of the maxilla		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Intellectual disability		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Intellectual disability		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Low-set ears		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Microphthalmia		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Microphthalmia		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Pectoral muscle hypoplasia/aplasia		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Pericallosal lipoma		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Posteriorly rotated ears		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Posteriorly rotated ears		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Preauricular skin tag		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Prominent glabella		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Ptosis		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Sparse eyebrow		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Sparse eyelashes		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Sparse eyelashes		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Tessier cleft		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Tessier cleft		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Tetralogy of Fallot		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Underdeveloped nasal alae		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Underdeveloped nasal alae		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Upper eyelid coloboma		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Wide nasal bridge		IAGP		8699517		HPO	MIM:613456
ALX1	Human	Wide nasal bridge		IAGP		8699517		HPO	ORPHA:306542
ALX1	Human	Widow's peak		IAGP		8699517		HPO	ORPHA:306542

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
ALX1	Human	Lung adenocarcinoma		IAGP	(Homo sapiens)	8554872	ClinVar Annotator: match by term: Lung adenocarcinoma	ClinVar	PMID:27993330

#	Reference Title	Reference Citation
1.	GOAs Human GO annotations	GOA_HUMAN data from the GO Consortium
2.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
3.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
5.	RGD HPO Phenotype Annotation Pipeline	RGD automated import pipeline for human HPO-to-gene-to-disease annotations
6.	Prenatal folic acid treatment suppresses acrania and meroanencephaly in mice mutant for the Cart1 homeobox gene.	Zhao Q, etal., Nat Genet 1996 Jul;13(3):275-83.

PMID:7592751	PMID:7690966	PMID:8756334	PMID:9753625	PMID:9847249	PMID:12477932	PMID:12929931	PMID:15489334	PMID:16189514	PMID:18029348	PMID:18976975	PMID:19274049
PMID:20398657	PMID:20451171	PMID:20932315	PMID:21873635	PMID:23288509	PMID:24081945	PMID:25736924	PMID:26722397	PMID:27053613	PMID:27324866	PMID:28473536	PMID:29490077
PMID:29936472	PMID:30773258	PMID:31182584	PMID:32296183	PMID:32344865	PMID:33961781	PMID:34104082	PMID:38334954

ALX1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	85,280,220 - 85,301,784 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	85,280,220 - 85,301,784 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	85,673,998 - 85,695,562 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	84,198,167 - 84,219,693 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	84,176,352 - 84,198,027	NCBI
Celera	12	85,337,491 - 85,358,941 (+)	NCBI		Celera
Cytogenetic Map	12	q21.31	NCBI
HuRef	12	82,731,405 - 82,752,155 (+)	NCBI		HuRef
CHM1_1	12	85,638,988 - 85,660,512 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	85,260,566 - 85,282,129 (+)	NCBI		T2T-CHM13v2.0

Alx1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	102,834,564 - 102,865,501 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	10	102,834,568 - 102,866,076 (-)	Ensembl		GRCm39 Ensembl
GRCm38	10	103,007,847 - 103,029,549 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	102,998,707 - 103,030,215 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	102,470,481 - 102,491,411 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	10	102,437,535 - 102,458,465 (-)	NCBI		MGSCv36	mm8
Celera	10	104,953,109 - 104,974,249 (-)	NCBI		Celera
Cytogenetic Map	10	D1	NCBI
cM Map	10	53.56	NCBI

Alx1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	40,044,185 - 40,063,778 (-)	NCBI		GRCr8
mRatBN7.2	7	38,157,626 - 38,177,220 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	38,147,117 - 38,177,220 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	40,097,722 - 40,117,118 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	42,300,790 - 42,320,186 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	42,075,714 - 42,095,110 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	44,751,865 - 44,771,458 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	44,751,873 - 44,771,458 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	44,776,471 - 44,796,064 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	41,090,481 - 41,110,281 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	7	41,110,754 - 41,130,552 (-)	NCBI
Celera	7	35,109,882 - 35,129,389 (-)	NCBI		Celera
Cytogenetic Map	7	q21	NCBI

ALX1
(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	10	93,330,838 - 93,352,596 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	93,327,236 - 93,348,994 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	82,800,273 - 82,822,031 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	85,902,113 - 85,923,781 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	85,902,113 - 85,923,774 (+)	Ensembl	panpan1.1		panPan2

ALX1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	15	26,838,615 - 26,858,786 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	15	26,834,670 - 26,858,803 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	15	27,282,241 - 27,303,179 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	15	27,452,234 - 27,473,164 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	15	27,451,887 - 27,473,181 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	15	26,804,074 - 26,825,013 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	15	26,844,249 - 26,865,196 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	15	27,092,976 - 27,113,925 (+)	NCBI		UU_Cfam_GSD_1.0

Alx1
(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	33,438,371 - 33,460,018 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936507	2,775,752 - 2,797,062 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936507	2,775,752 - 2,797,065 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ALX1
(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	96,763,685 - 96,785,165 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	96,761,683 - 96,785,125 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	101,496,883 - 101,518,746 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ALX1
(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	11	80,687,799 - 80,717,886 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	80,696,271 - 80,717,574 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	164,616,871 - 164,638,679 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants in ALX1
42 total Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
NM_006982.3(ALX1):c.531+1G>A	single nucleotide variant	Frontonasal dysplasia - severe microphthalmia - severe facial clefting syndrome [RCV000008579]	Chr12:85283877 [GRCh38] Chr12:85677655 [GRCh37] Chr12:12q21.31	pathogenic
GRCh38/hg38 12q21.2-21.31(chr12:77564757-85370822)x3	copy number gain	See cases [RCV000053684]	Chr12:77564757..85370822 [GRCh38] Chr12:77958537..85764600 [GRCh37] Chr12:76482668..84288731 [NCBI36] Chr12:12q21.2-21.31	pathogenic
GRCh38/hg38 12q21.31(chr12:85253355-85319830)x1	copy number loss	See cases [RCV000136604]	Chr12:85253355..85319830 [GRCh38] Chr12:85647133..85713608 [GRCh37] Chr12:84171264..84237739 [NCBI36] Chr12:12q21.31	uncertain significance
GRCh38/hg38 12q21.31(chr12:85228467-85675435)x1	copy number loss	See cases [RCV000137317]	Chr12:85228467..85675435 [GRCh38] Chr12:85622245..86069213 [GRCh37] Chr12:84146376..84593344 [NCBI36] Chr12:12q21.31	uncertain significance
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3	copy number gain	See cases [RCV000139555]	Chr12:121271..133196807 [GRCh38] Chr12:282465..133773393 [GRCh37] Chr12:100698..132283466 [NCBI36] Chr12:12p13.33-q24.33	pathogenic
GRCh38/hg38 12q21.1-22(chr12:73485697-92795805)x1	copy number loss	See cases [RCV000143099]	Chr12:73485697..92795805 [GRCh38] Chr12:73879477..93189581 [GRCh37] Chr12:72165744..91713712 [NCBI36] Chr12:12q21.1-22	pathogenic
NM_006982.3(ALX1):c.190C>T (p.Arg64Cys)	single nucleotide variant	ALX1-related disorder [RCV003927755]\|not provided [RCV000883228]\|not specified [RCV000195110]	Chr12:85280451 [GRCh38] Chr12:85674229 [GRCh37] Chr12:12q21.31	benign\|likely benign\|uncertain significance
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3	copy number gain	See cases [RCV000258805]	Chr12:1..133851895 [GRCh37] Chr12:12p13.33-q24.33	pathogenic\|likely pathogenic
NM_006982.3(ALX1):c.191G>T (p.Arg64Leu)	single nucleotide variant	ALX1-related disorder [RCV003920126]\|Frontonasal dysplasia - severe microphthalmia - severe facial clefting syndrome [RCV000415504]\|not provided [RCV000959928]\|not specified [RCV000353018]	Chr12:85280452 [GRCh38] Chr12:85674230 [GRCh37] Chr12:12q21.31	pathogenic\|benign\|likely benign
NM_006982.3(ALX1):c.151C>T (p.Gln51Ter)	single nucleotide variant	Frontonasal dysplasia - severe microphthalmia - severe facial clefting syndrome [RCV003314275]	Chr12:85280412 [GRCh38] Chr12:85674190 [GRCh37] Chr12:12q21.31	likely pathogenic
GRCh37/hg19 12q21.31(chr12:85658740-85692582)x1	copy number loss	See cases [RCV000446255]	Chr12:85658740..85692582 [GRCh37] Chr12:12q21.31	uncertain significance
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3	copy number gain	See cases [RCV000510482]	Chr12:173787..133777902 [GRCh37] Chr12:12p13.33-q24.33	pathogenic
NM_006982.3(ALX1):c.413C>T (p.Thr138Ile)	single nucleotide variant	not specified [RCV000502614]	Chr12:85283758 [GRCh38] Chr12:85677536 [GRCh37] Chr12:12q21.31	uncertain significance
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)	copy number gain	See cases [RCV000511643]	Chr12:173787..133777902 [GRCh37] Chr12:12p13.33-q24.33	pathogenic
GRCh37/hg19 12q21.31(chr12:85191032-85746665)x3	copy number gain	See cases [RCV000511483]	Chr12:85191032..85746665 [GRCh37] Chr12:12q21.31	uncertain significance
GRCh37/hg19 12q21.31(chr12:83266252-86018250)x3	copy number gain	not provided [RCV000659222]	Chr12:83266252..86018250 [GRCh37] Chr12:12q21.31	uncertain significance
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3	copy number gain	not provided [RCV000750246]	Chr12:191619..133777645 [GRCh37] Chr12:12p13.33-q24.33	pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3	copy number gain	not provided [RCV000750253]	Chr12:621220..133779118 [GRCh37] Chr12:12p13.33-q24.33	pathogenic
GRCh37/hg19 12q15-21.33(chr12:69608090-89629345)x1	copy number loss	not provided [RCV000737927]	Chr12:69608090..89629345 [GRCh37] Chr12:12q15-21.33	pathogenic
GRCh37/hg19 12q21.31(chr12:85680695-85741610)x3	copy number gain	not provided [RCV000750494]	Chr12:85680695..85741610 [GRCh37] Chr12:12q21.31	benign
NM_006982.3(ALX1):c.630A>T (p.Ser210=)	single nucleotide variant	not provided [RCV000970871]	Chr12:85286951 [GRCh38] Chr12:85680729 [GRCh37] Chr12:12q21.31	benign
NM_006982.3(ALX1):c.182A>G (p.His61Arg)	single nucleotide variant	not provided [RCV000949564]	Chr12:85280443 [GRCh38] Chr12:85280443..85280444 [GRCh38] Chr12:85674221 [GRCh37] Chr12:85674221..85674222 [GRCh37] Chr12:12q21.31	benign
GRCh37/hg19 12q21.31-21.32(chr12:82183041-88755577)	copy number gain	not provided [RCV000767570]	Chr12:82183041..88755577 [GRCh37] Chr12:12q21.31-21.32	pathogenic
NM_006982.3(ALX1):c.597G>A (p.Ala199=)	single nucleotide variant	not provided [RCV000973499]	Chr12:85286918 [GRCh38] Chr12:85680696 [GRCh37] Chr12:12q21.31	benign
NM_006982.3(ALX1):c.266A>G (p.His89Arg)	single nucleotide variant	not provided [RCV000965903]	Chr12:85283611 [GRCh38] Chr12:85677389 [GRCh37] Chr12:12q21.31	benign
GRCh37/hg19 12q21.31(chr12:85187541-85749398)x3	copy number gain	not provided [RCV000848015]	Chr12:85187541..85749398 [GRCh37] Chr12:12q21.31	uncertain significance
GRCh37/hg19 12q21.2-22(chr12:77737623-94330526)x1	copy number loss	not provided [RCV000848027]	Chr12:77737623..94330526 [GRCh37] Chr12:12q21.2-22	pathogenic
GRCh37/hg19 12q21.31(chr12:85639742-85689049)x1	copy number loss	not provided [RCV000847010]	Chr12:85639742..85689049 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.357T>A (p.Leu119=)	single nucleotide variant	ALX1-related disorder [RCV003910581]\|not provided [RCV000890973]	Chr12:85283702 [GRCh38] Chr12:85677480 [GRCh37] Chr12:12q21.31	likely benign
NM_006982.3(ALX1):c.226+193C>A	single nucleotide variant	not provided [RCV001615578]	Chr12:85280680 [GRCh38] Chr12:85674458 [GRCh37] Chr12:12q21.31	benign
NM_006982.3(ALX1):c.661-1G>C	single nucleotide variant	Frontonasal dysplasia - severe microphthalmia - severe facial clefting syndrome [RCV001027524]	Chr12:85301154 [GRCh38] Chr12:85694932 [GRCh37] Chr12:12q21.31	pathogenic
NM_006982.3(ALX1):c.532-97dup	duplication	not provided [RCV001612226]	Chr12:85286749..85286750 [GRCh38] Chr12:85680527..85680528 [GRCh37] Chr12:12q21.31	benign
GRCh37/hg19 12q21.31(chr12:85658740-85692582)	copy number loss	not specified [RCV002053005]	Chr12:85658740..85692582 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.532-11T>G	single nucleotide variant	not provided [RCV002862891]	Chr12:85286842 [GRCh38] Chr12:85680620 [GRCh37] Chr12:12q21.31	likely benign
NM_006982.3(ALX1):c.705G>A (p.Val235=)	single nucleotide variant	not provided [RCV002681346]	Chr12:85301199 [GRCh38] Chr12:85694977 [GRCh37] Chr12:12q21.31	likely benign
NM_006982.3(ALX1):c.532-17T>C	single nucleotide variant	not provided [RCV002776391]	Chr12:85286836 [GRCh38] Chr12:85680614 [GRCh37] Chr12:12q21.31	benign
NM_006982.3(ALX1):c.660+17A>G	single nucleotide variant	not provided [RCV002771339]	Chr12:85286998 [GRCh38] Chr12:85680776 [GRCh37] Chr12:12q21.31	benign
GRCh37/hg19 12q21.31(chr12:85404081-85694726)x3	copy number gain	not provided [RCV002475594]	Chr12:85404081..85694726 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.694G>T (p.Gly232Cys)	single nucleotide variant	Inborn genetic diseases [RCV002972830]	Chr12:85301188 [GRCh38] Chr12:85694966 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.190C>A (p.Arg64Ser)	single nucleotide variant	Inborn genetic diseases [RCV002707753]	Chr12:85280451 [GRCh38] Chr12:85674229 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.769C>T (p.Arg257Trp)	single nucleotide variant	Inborn genetic diseases [RCV002737743]	Chr12:85301263 [GRCh38] Chr12:85695041 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.149T>C (p.Val50Ala)	single nucleotide variant	Inborn genetic diseases [RCV004641964]\|not specified [RCV002510309]	Chr12:85280410 [GRCh38] Chr12:85674188 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.145T>A (p.Cys49Ser)	single nucleotide variant	Inborn genetic diseases [RCV002784666]	Chr12:85280406 [GRCh38] Chr12:85674184 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.150G>T (p.Val50=)	single nucleotide variant	not provided [RCV002954430]	Chr12:85280411 [GRCh38] Chr12:85674189 [GRCh37] Chr12:12q21.31	likely benign
NM_006982.3(ALX1):c.770G>C (p.Arg257Pro)	single nucleotide variant	Inborn genetic diseases [RCV003250651]\|not provided [RCV002959039]	Chr12:85301264 [GRCh38] Chr12:85695042 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.48A>G (p.Lys16=)	single nucleotide variant	not provided [RCV002890535]	Chr12:85280309 [GRCh38] Chr12:85674087 [GRCh37] Chr12:12q21.31	benign
NM_006982.3(ALX1):c.288G>A (p.Met96Ile)	single nucleotide variant	Inborn genetic diseases [RCV002892297]	Chr12:85283633 [GRCh38] Chr12:85677411 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.23T>C (p.Phe8Ser)	single nucleotide variant	Inborn genetic diseases [RCV002877746]	Chr12:85280284 [GRCh38] Chr12:85674062 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.791G>T (p.Gly264Val)	single nucleotide variant	Lung adenocarcinoma [RCV003129711]	Chr12:85301285 [GRCh38] Chr12:85695063 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.286A>G (p.Met96Val)	single nucleotide variant	Inborn genetic diseases [RCV003254363]	Chr12:85283631 [GRCh38] Chr12:85677409 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.709A>T (p.Thr237Ser)	single nucleotide variant	Inborn genetic diseases [RCV003220032]	Chr12:85301203 [GRCh38] Chr12:85694981 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.377A>G (p.Asn126Ser)	single nucleotide variant	Inborn genetic diseases [RCV003183458]	Chr12:85283722 [GRCh38] Chr12:85677500 [GRCh37] Chr12:12q21.31	uncertain significance
GRCh37/hg19 12q21.31(chr12:80647969-85713707)x1	copy number loss	not provided [RCV003483158]	Chr12:80647969..85713707 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.356T>G (p.Leu119Arg)	single nucleotide variant	not provided [RCV003548493]	Chr12:85283701 [GRCh38] Chr12:85677479 [GRCh37] Chr12:12q21.31	likely benign
NM_006982.3(ALX1):c.414C>T (p.Thr138=)	single nucleotide variant	not provided [RCV003717560]	Chr12:85283759 [GRCh38] Chr12:85677537 [GRCh37] Chr12:12q21.31	likely benign
NM_006982.3(ALX1):c.957C>T (p.Thr319=)	single nucleotide variant	not provided [RCV003726343]	Chr12:85301451 [GRCh38] Chr12:85695229 [GRCh37] Chr12:12q21.31	likely benign
GRCh37/hg19 12q21.1-21.33(chr12:74887087-90469800)x1	copy number loss	not specified [RCV003986972]	Chr12:74887087..90469800 [GRCh37] Chr12:12q21.1-21.33	pathogenic
NM_006982.3(ALX1):c.801C>T (p.Asn267=)	single nucleotide variant	not provided [RCV003822652]	Chr12:85301295 [GRCh38] Chr12:85695073 [GRCh37] Chr12:12q21.31	likely benign
NM_006982.3(ALX1):c.507A>G (p.Thr169=)	single nucleotide variant	ALX1-related disorder [RCV003904513]	Chr12:85283852 [GRCh38] Chr12:85677630 [GRCh37] Chr12:12q21.31	likely benign
NC_000012.11:g.(?_85673997)_(85695563_?)del	deletion	Frontonasal dysplasia - severe microphthalmia - severe facial clefting syndrome [RCV003995123]	Chr12:85673997..85695563 [GRCh37] Chr12:12q21.31	pathogenic
NM_006982.3(ALX1):c.109A>G (p.Asn37Asp)	single nucleotide variant	Inborn genetic diseases [RCV004411718]	Chr12:85280370 [GRCh38] Chr12:85674148 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.554C>T (p.Ala185Val)	single nucleotide variant	Inborn genetic diseases [RCV004636286]	Chr12:85286875 [GRCh38] Chr12:85680653 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.108C>G (p.Asp36Glu)	single nucleotide variant	Inborn genetic diseases [RCV004983993]	Chr12:85280369 [GRCh38] Chr12:85674147 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.637C>T (p.Pro213Ser)	single nucleotide variant	Inborn genetic diseases [RCV004983992]	Chr12:85286958 [GRCh38] Chr12:85680736 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.697G>T (p.Gly233Cys)	single nucleotide variant	Inborn genetic diseases [RCV004983991]	Chr12:85301191 [GRCh38] Chr12:85694969 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.767C>T (p.Pro256Leu)	single nucleotide variant	Inborn genetic diseases [RCV004983990]	Chr12:85301261 [GRCh38] Chr12:85695039 [GRCh37] Chr12:12q21.31	uncertain significance
NM_006982.3(ALX1):c.318C>T (p.Pro106=)	single nucleotide variant	not provided [RCV005074097]	Chr12:85283663 [GRCh38] Chr12:85677441 [GRCh37] Chr12:12q21.31	likely benign
NM_006982.3(ALX1):c.282A>C (p.Arg94Ser)	single nucleotide variant	not provided [RCV005184699]	Chr12:85283627 [GRCh38] Chr12:85677405 [GRCh37] Chr12:12q21.31	likely benign

Predicted Target Of

	Summary Value
Count of predictions:	85
Count of miRNA genes:	76
Interacting mature miRNAs:	84
Transcripts:	ENST00000316824
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.

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
597227867	GWAS1323941_H	protein measurement QTL GWAS1323941 (human)		2e-09	protein measurement		12	85280443	85280444	Human

RH68918

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	12	85,685,763 - 85,685,921	UniSTS	GRCh37
Build 36	12	84,209,894 - 84,210,052	RGD	NCBI36
Celera	12	85,349,142 - 85,349,300	RGD
Cytogenetic Map	12	q21.31	UniSTS
HuRef	12	82,742,357 - 82,742,515	UniSTS
GeneMap99-GB4 RH Map	12	336.6	UniSTS
NCBI RH Map	12	593.5	UniSTS

STS-N20106

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	12	85,695,336 - 85,695,472	UniSTS	GRCh37
Build 36	12	84,219,467 - 84,219,603	RGD	NCBI36
Celera	12	85,358,715 - 85,358,851	RGD
Cytogenetic Map	12	q21.31	UniSTS
HuRef	12	82,751,929 - 82,752,065	UniSTS
GeneMap99-GB4 RH Map	12	336.49	UniSTS
NCBI RH Map	12	593.5	UniSTS

CART1__4510

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	12	85,695,002 - 85,695,642	UniSTS	GRCh37
Build 36	12	84,219,133 - 84,219,773	RGD	NCBI36
Celera	12	85,358,381 - 85,359,021	RGD
HuRef	12	82,751,595 - 82,752,235	UniSTS

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

adipose tissue	alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	entire extraembryonic component	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
690	993	2108	1295	3367	959	1258	2	226	210	67	2153	2867	2842	35	2187	644	1518	1011	166	1


RefSeq Transcripts	NG_023202	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_006982	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_011538782	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC127069	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC131532	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC133794	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ558236	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ558237	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC010923	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH471054	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068266	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	EU794597	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U31986	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENST00000316824 ⟹ ENSP00000315417

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	85,280,220 - 85,301,784 (+)	Ensembl

RefSeq Acc Id:

NM_006982 ⟹ NP_008913

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	12	85,280,220 - 85,301,784 (+)	NCBI
GRCh37	12	85,673,713 - 85,695,562 (+)	NCBI
Build 36	12	84,198,167 - 84,219,693 (+)	NCBI Archive
Celera	12	85,337,491 - 85,358,941 (+)	RGD
HuRef	12	82,731,405 - 82,752,155 (+)	ENTREZGENE
CHM1_1	12	85,638,988 - 85,660,512 (+)	NCBI
T2T-CHM13v2.0	12	85,260,566 - 85,282,129 (+)	NCBI

Sequence:

show sequence

AGTTTCTGTGCCCCAGGAGCTACGCGACAGTCTTCCAGGATTATGGAGTTTCTGAGCGAGAAGTTTGCCCTCAAGAGCCCTCCGAGTAAAAACAGTGACTTTTACATGGGCGCAGGAGGTCCTCTGGA
GCACGTTATGGAGACGCTGGACAATGAGTCCTTTTACAGCAAAGCGTCTGCAGGCAAATGCGTGCAGGCCTTCGGACCCCTGCCCCGCGCCGAGCATCACGTGCGCTTGGAGAGGACCTCGCCCTGTC
AGGACAGCAGCGTGAACTATGGGATCACTAAAGTAGAAGGACAGCCCCTTCACACCGAACTGAATAGAGCTATGGACAACTGTAACAGTCTCCGAATGTCTCCCGTGAAAGGGATGCAAGAGAAGGGA
GAGCTGGATGAACTTGGGGATAAATGTGATAGCAATGTATCCAGCAGTAAGAAACGGAGGCACCGAACCACCTTCACCAGTTTGCAGCTAGAGGAGCTGGAGAAAGTCTTTCAGAAAACTCATTACCC
GGATGTGTATGTCAGAGAACAGCTTGCTCTGAGGACAGAGCTCACTGAGGCCAGGGTCCAGGTTTGGTTTCAAAATCGAAGGGCCAAATGGAGAAAAAGGGAACGTTATGGCCAAATACAACAAGCGA
AAAGCCATTTTGCTGCCACCTATGATATATCAGTTTTGCCAAGGACTGACAGCTACCCACAGATTCAGAACAATTTGTGGGCAGGAAATGCAAGTGGTGGTTCTGTGGTTACTTCATGCATGTTACCA
CGTGACACTTCCTCCTGTATGACACCTTATTCTCACTCGCCTCGGACAGATTCCAGTTACACGGGGTTTTCAAACCACCAGAACCAGTTCAGCCACGTGCCCCTCAACAATTTTTTCACTGACTCTCT
TCTTACTGGGGCAACCAATGGACATGCATTTGAAACAAAGCCAGAGTTTGAAAGGAGGTCTTCCAGTATCGCAGTTCTTCGAATGAAAGCCAAGGAGCACACCGCCAATATTTCATGGGCCATGTAAC
ATACAGTACTCTTTTATTTTTCTTTTAATAGCAAAGTTAAACATTCTTATTTCTCATATTTAAAGGATACCACAATAAGCTGCTGTGTGTGGAATTGCTAAAGGTCAAGATATTCAGTGAGACCAGCT
TAAATGAATAGTTGTTATTTAACATTAAAATCTAAGAATGAACCTCTGAAAAGACTAAATAGGTTTACCATGTGCCAGTCTCCACAAACCCTGTTTTAGTAGTAAGGTTTTCTTTTTCTATTGTACAA
GTCAATGAAATATGATCACGCAACTTATTAAAGAATAAATGTGTTAAACAAA

hide sequence


Protein RefSeqs	NP_008913	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB08960	(Get FASTA)	NCBI Sequence Viewer
	AAH10923	(Get FASTA)	NCBI Sequence Viewer
	ACJ13651	(Get FASTA)	NCBI Sequence Viewer
	CAD90155	(Get FASTA)	NCBI Sequence Viewer
	EAW97398	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSP00000315417
	ENSP00000315417.3
GenBank Protein	Q15699	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_008913 ⟸ NM_006982

- UniProtKB:

Q546C8 (UniProtKB/Swiss-Prot), Q96FH4 (UniProtKB/Swiss-Prot), Q15699 (UniProtKB/Swiss-Prot), V9HWA7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MEFLSEKFALKSPPSKNSDFYMGAGGPLEHVMETLDNESFYSKASAGKCVQAFGPLPRAEHHVRLERTSPCQDSSVNYGITKVEGQPLHTELNRAMDNCNSLRMSPVKGMQEKGELDELGDKCDSNVS
SSKKRRHRTTFTSLQLEELEKVFQKTHYPDVYVREQLALRTELTEARVQVWFQNRRAKWRKRERYGQIQQAKSHFAATYDISVLPRTDSYPQIQNNLWAGNASGGSVVTSCMLPRDTSSCMTPYSHSP
RTDSSYTGFSNHQNQFSHVPLNNFFTDSLLTGATNGHAFETKPEFERRSSSIAVLRMKAKEHTANISWAM

hide sequence

Ensembl Acc Id:

ENSP00000315417 ⟸ ENST00000316824

Protein Domains

Homeobox OAR

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q15699-F1-model_v2	AlphaFold	Q15699	1-326	view protein structure

RGD ID:

6789644

Promoter ID:

HG_KWN:16262

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

HeLa_S3

Transcripts:

ENST00000316824

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	12	84,198,231 - 84,198,731 (+)	MPROMDB

RGD ID:

7224939

Promoter ID:

EPDNEW_H18215

Type:

initiation region

Name:

ALX1_1

Description:

ALX homeobox 1

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_H18216

Experiment Methods:

Single-end sequencing.; Paired-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	12	85,280,098 - 85,280,158	EPDNEW

RGD ID:

7224943

Promoter ID:

EPDNEW_H18216

Type:

initiation region

Name:

ALX1_2

Description:

ALX homeobox 1

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_H18215

Experiment Methods:

Single-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	12	85,280,248 - 85,280,308	EPDNEW

Database	Acc Id	Source(s)
COSMIC	ALX1	COSMIC
Ensembl Genes	ENSG00000180318	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENST00000316824	ENTREZGENE
	ENST00000316824.4	UniProtKB/Swiss-Prot
Gene3D-CATH	Homeodomain-like	UniProtKB/Swiss-Prot
GTEx	ENSG00000180318	GTEx
HGNC ID	HGNC:1494	ENTREZGENE
Human Proteome Map	ALX1	Human Proteome Map
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot
	Homeobox_CS	UniProtKB/Swiss-Prot
	Homeobox_dom	UniProtKB/Swiss-Prot
	OAR_dom	UniProtKB/Swiss-Prot
	Paired_Homeobox_TFs	UniProtKB/Swiss-Prot
KEGG Report	hsa:8092	UniProtKB/Swiss-Prot
NCBI Gene	8092	ENTREZGENE
OMIM	601527	OMIM
PANTHER	HOMEOBOX PROTEIN ARISTALESS	UniProtKB/Swiss-Prot
	PTHR24329:SF359	UniProtKB/Swiss-Prot
Pfam	Homeodomain	UniProtKB/Swiss-Prot
	OAR	UniProtKB/Swiss-Prot
PharmGKB	PA162376294	PharmGKB
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot
	HOMEOBOX_2	UniProtKB/Swiss-Prot
	OAR	UniProtKB/Swiss-Prot
SMART	HOX	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot
UniProt	ALX1_HUMAN	UniProtKB/Swiss-Prot, ENTREZGENE
	Q546C8	ENTREZGENE
	Q96FH4	ENTREZGENE
	V9HWA7	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	Q546C8	UniProtKB/Swiss-Prot
	Q96FH4	UniProtKB/Swiss-Prot

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


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


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