HOXA7

homeobox A7, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 7:27153716-27157936

Previous symbols: [ "HOX1A", "HOX1" ]

Links

ENSG00000122592

∙ NCBI:3204 ∙ OMIM:142950 ∙ HGNC:5108 ∙ Uniprot:P31268 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HOXA7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXA7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14 clinvar	1 clinvar		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in HOXA7

This is a list of pathogenic ClinVar variants found in the HOXA7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
7-27154939-A-T	not specified	Likely benign (Sep 13, 2023)	2589690
7-27154977-C-T	not specified	Uncertain significance (Aug 02, 2021)	2265726
7-27154980-C-T	not specified	Uncertain significance (Mar 07, 2024)	3106600
7-27154985-G-A	not specified	Uncertain significance (Sep 16, 2021)	2250299
7-27155001-C-G	not specified	Uncertain significance (Jul 21, 2021)	2275629
7-27155061-G-C	not specified	Uncertain significance (Nov 04, 2022)	2321694
7-27155115-T-C	not specified	Uncertain significance (Oct 20, 2021)	2255957
7-27155145-G-C	not specified	Uncertain significance (Aug 22, 2022)	2225613
7-27155189-G-A	not specified	Uncertain significance (Jan 03, 2024)	3106599
7-27156285-T-G	not specified	Uncertain significance (Apr 19, 2024)	3284646
7-27156290-C-T	not specified	Uncertain significance (Jan 23, 2024)	3106598
7-27156361-T-C	not specified	Uncertain significance (Nov 17, 2022)	2326535
7-27156425-C-G	not specified	Uncertain significance (Sep 28, 2022)	2393137
7-27156444-G-T	not specified	Uncertain significance (Dec 01, 2023)	3106597
7-27156457-G-A	not specified	Uncertain significance (Apr 23, 2024)	3284645
7-27156461-A-C	not specified	Uncertain significance (Jun 12, 2023)	2555029
7-27156487-A-C	not specified	Uncertain significance (Sep 14, 2023)	2624059

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXA7	protein_coding	protein_coding	ENST00000242159	2	4221

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00136	0.675	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.632	159	138	1.15	0.00000672	1488
Missense in Polyphen		48	42.771	1.1223		481
Synonymous	-1.77	80	62.2	1.29	0.00000330	455
Loss of Function	0.701	5	7.00	0.714	3.01e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000921	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000992	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000985	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.;
Pathway: miR-targeted genes in squamous cell - TarBase;keratinocyte differentiation (Consensus)

Recessive Scores

pRec: 0.110

Intolerance Scores

loftool: 0.456
rvis_EVS: 0.22
rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

pHI: 0.776
hipred: Y
hipred_score: 0.583
ghis: 0.456

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.555

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Hoxa7
Phenotype: normal phenotype; hematopoietic system phenotype; skeleton phenotype; immune system phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;angiogenesis;negative regulation of cell-matrix adhesion;negative regulation of leukocyte migration;anterior/posterior pattern specification;negative regulation of keratinocyte differentiation;negative regulation of monocyte differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;stem cell differentiation
Cellular component: nucleus;nucleoplasm;nuclear membrane
Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;transcription factor binding;sequence-specific DNA binding