HOXA10

homeobox A10, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 7:27170604-27180261

Previous symbols: [ "HOX1H", "HOX1" ]

Links

ENSG00000253293 ∙ NCBI:3206 ∙ OMIM:142957 ∙ HGNC:5100 ∙ Uniprot:P31260 ∙ 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 HOXA10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXA10 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				5	3	8
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	30	7	4

Variants in HOXA10

This is a list of pathogenic ClinVar variants found in the HOXA10 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-27171929-C-T		HOXA10-related disorder	Benign (Apr 10, 2019)
7-27171965-C-T		Inborn genetic diseases	Uncertain significance (Sep 25, 2023)
7-27171997-G-C		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
7-27173340-C-A		HOXA10-related disorder	Benign (Jul 31, 2019)
7-27173369-G-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2023)
7-27173377-G-C		Inborn genetic diseases	Uncertain significance (Apr 24, 2024)
7-27173394-C-T		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
7-27173397-G-A		Inborn genetic diseases	Uncertain significance (Dec 27, 2022)
7-27173460-C-A		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
7-27173482-G-C		HOXA10-related disorder	Likely benign (Jul 01, 2019)
7-27173502-C-A		Inborn genetic diseases	Uncertain significance (Jun 09, 2022)
7-27173504-C-G		Inborn genetic diseases	Uncertain significance (Aug 17, 2021)
7-27173504-C-T		Inborn genetic diseases	Uncertain significance (Jul 05, 2023)
7-27173514-G-C		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
7-27173521-A-C		Inborn genetic diseases	Uncertain significance (Mar 28, 2024)
7-27173523-C-T		Inborn genetic diseases	Uncertain significance (Jul 12, 2022)
7-27173565-G-T		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
7-27173569-C-A		HOXA10-related disorder	Benign (Jul 12, 2019)
7-27173570-G-A		Inborn genetic diseases	Uncertain significance (Nov 06, 2023)
7-27173608-C-A		HOXA10-related disorder	Benign (Jan 14, 2020)
7-27173609-G-A		Inborn genetic diseases	Uncertain significance (May 26, 2024)
7-27173621-C-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
7-27173637-T-C		Inborn genetic diseases	Uncertain significance (Dec 06, 2023)
7-27173638-G-A		HOXA10-related disorder	Likely benign (Mar 13, 2019)
7-27173646-C-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXA10	protein_coding	protein_coding	ENST00000283921	2	9671

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.885	0.115	125745	0	3	125748	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.07	258	214	1.21	0.00000996	2530
Missense in Polyphen		43	61.367	0.7007		755
Synonymous	-2.35	131	101	1.30	0.00000494	904
Loss of Function	2.86	1	11.4	0.0876	5.05e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000276	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. Binds to the DNA sequence 5'-AA[AT]TTTTATTAC-3'.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Signaling events mediated by HDAC Class III (Consensus)

Haploinsufficiency Scores

• pHI: 0.998
• hipred: Y
• hipred_score: 0.776
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxa10
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype; reproductive system phenotype

Gene ontology

• Biological process: skeletal system development;multicellular organism development;spermatogenesis;single fertilization;male gonad development;anterior/posterior pattern specification;proximal/distal pattern formation;embryonic limb morphogenesis;positive regulation of transcription by RNA polymerase II;uterus development
• Cellular component: nucleus;transcription factor complex;cytoplasm
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;histone deacetylase binding