HOXA6

homeobox A6, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 7:27145395-27150603

Previous symbols: [ "HOX1B", "HOX1" ]

Links

ENSG00000106006 ∙ NCBI:3203 ∙ OMIM:142951 ∙ HGNC:5107 ∙ Uniprot:P31267 ∙ 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 HOXA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXA6 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			15			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	15	0	0

Variants in HOXA6

This is a list of pathogenic ClinVar variants found in the HOXA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-27145684-C-T		not specified	Uncertain significance (Sep 06, 2022)
7-27145690-C-A		not specified	Uncertain significance (Feb 28, 2023)
7-27145692-C-A		not specified	Uncertain significance (Mar 18, 2024)
7-27145704-G-A		not specified	Uncertain significance (May 16, 2022)
7-27145708-T-C		not specified	Uncertain significance (Mar 31, 2023)
7-27145744-G-C		not specified	Uncertain significance (Jan 24, 2024)
7-27145801-C-T		not specified	Uncertain significance (Jul 08, 2022)
7-27145802-G-C		not specified	Uncertain significance (Jun 10, 2024)
7-27145858-G-T		not specified	Uncertain significance (Aug 29, 2022)
7-27145869-C-A		not specified	Uncertain significance (Apr 12, 2022)
7-27145870-G-A		not specified	Uncertain significance (May 30, 2022)
7-27147348-G-T		not specified	Uncertain significance (Dec 16, 2022)
7-27147355-T-C		not specified	Uncertain significance (Oct 10, 2023)
7-27147457-C-T		not specified	Uncertain significance (Sep 18, 2023)
7-27147533-C-G		not specified	Uncertain significance (Dec 02, 2022)
7-27147640-G-T		not specified	Uncertain significance (Nov 07, 2022)
7-27147661-G-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXA6	protein_coding	protein_coding	ENST00000222728	2	5208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000299	0.338	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0979	154	151	1.02	0.00000969	1519
Missense in Polyphen		90	83.933	1.0723		797
Synonymous	0.989	56	66.2	0.845	0.00000434	456
Loss of Function	0.327	9	10.1	0.889	4.94e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
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.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.456
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.396
• hipred: N
• hipred_score: 0.469
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxa6
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: anterior/posterior pattern specification;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis
• Cellular component: nucleus
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific