HOXA4

homeobox A4, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 7:27128507-27130780

Previous symbols: [ "HOX1D", "HOX1" ]

Links

ENSG00000197576 ∙ NCBI:3201 ∙ OMIM:142953 ∙ HGNC:5105 ∙ Uniprot:Q00056 ∙ 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 HOXA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXA4 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			1	4	1	6
missense			36	3	3	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					6	6
Total	0	0	37	7	10

Variants in HOXA4

This is a list of pathogenic ClinVar variants found in the HOXA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-27128893-C-G			Benign (Nov 12, 2018)
7-27128971-A-G			Benign (Nov 12, 2018)
7-27129100-C-T			Benign (Nov 12, 2018)
7-27129263-G-T		not specified	Uncertain significance (Jul 06, 2021)
7-27129268-T-C		not specified	Uncertain significance (Dec 21, 2022)
7-27129269-G-A		not specified	Uncertain significance (May 01, 2022)
7-27129277-A-C		not specified	Uncertain significance (Oct 26, 2022)
7-27129292-G-A		not specified	Uncertain significance (May 21, 2024)
7-27129301-T-C		not specified	Uncertain significance (Dec 21, 2022)
7-27129308-G-T		not specified	Uncertain significance (Feb 06, 2023)
7-27129343-C-G		not specified	Uncertain significance (Jun 29, 2023)
7-27129352-G-A		not specified	Uncertain significance (Oct 28, 2024)
7-27129365-T-C		not specified	Uncertain significance (Jan 03, 2022)
7-27129388-C-T		not specified	Uncertain significance (Jun 16, 2024)
7-27129415-T-C		not specified	Uncertain significance (Jun 29, 2023)
7-27129418-C-T		not specified	Uncertain significance (Sep 20, 2023)
7-27129461-G-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
7-27129474-T-G			Benign (Jun 09, 2021)
7-27129478-T-C		not specified	Uncertain significance (Mar 25, 2024)
7-27129518-G-A		not specified	Uncertain significance (Apr 25, 2022)
7-27129536-A-G		not specified	Uncertain significance (Dec 21, 2023)
7-27129538-C-A		not specified	Uncertain significance (Jun 22, 2021)
7-27129538-C-T		not specified	Uncertain significance (Aug 09, 2021)
7-27129544-G-C		not specified	Uncertain significance (Jan 03, 2024)
7-27129750-T-C			Benign (Jun 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXA4	protein_coding	protein_coding	ENST00000360046	2	2293

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000860	0.329	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.332	142	131	1.08	0.00000737	1952
Missense in Polyphen		48	39.879	1.2037		440
Synonymous	-0.272	61	58.4	1.05	0.00000322	663
Loss of Function	0.193	8	8.61	0.929	5.05e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000712	0.0000703
Middle Eastern	0.000111	0.000109
South Asian	0.0000980	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. Binds to sites in the 5'-flanking sequence of its coding region with various affinities. The consensus sequences of the high and low affinity binding sites are 5'-TAATGA[CG]-3' and 5'-CTAATTTT- 3'.
• Pathway: Activation of anterior HOX genes in hindbrain development during early embryogenesis (Consensus)

Haploinsufficiency Scores

• pHI: 0.439
• hipred: N
• hipred_score: 0.354
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.572

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxa4
• Phenotype: skeleton phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: skeletal system development;anatomical structure morphogenesis;anterior/posterior pattern specification;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis
• Cellular component: nucleus;nuclear body
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;activating transcription factor binding