HOXA3

homeobox A3, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 7:27106183-27152583

Previous symbols: [ "HOX1E", "HOX1" ]

Links

ENSG00000105997 ∙ NCBI:3200 ∙ OMIM:142954 ∙ HGNC:5104 ∙ Uniprot:O43365 ∙ 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 HOXA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXA3 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		1
missense			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			60	7	13	80
Total	0	0	92	10	13

Variants in HOXA3

This is a list of pathogenic ClinVar variants found in the HOXA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-27107937-G-A		not specified	Uncertain significance (Jan 24, 2023)
7-27107953-C-G		not specified	Uncertain significance (Dec 20, 2021)
7-27107985-T-C		not specified	Uncertain significance (Mar 21, 2023)
7-27107989-T-C		not specified	Uncertain significance (Mar 02, 2023)
7-27107999-C-G		not specified	Uncertain significance (Sep 26, 2022)
7-27108004-C-T		not specified	Uncertain significance (Oct 30, 2023)
7-27108081-G-C		not specified	Uncertain significance (Nov 10, 2022)
7-27108127-G-T		not specified	Uncertain significance (Dec 08, 2023)
7-27108135-T-A		not specified	Uncertain significance (Jul 14, 2021)
7-27108154-C-A		not specified	Uncertain significance (Jun 09, 2022)
7-27108208-G-A		not specified	Uncertain significance (Feb 27, 2024)
7-27108235-C-A		not specified	Uncertain significance (Oct 20, 2023)
7-27108274-G-T		not specified	Uncertain significance (May 20, 2024)
7-27108293-G-C		not specified	Uncertain significance (Dec 14, 2022)
7-27108310-G-T		not specified	Uncertain significance (Dec 20, 2023)
7-27108337-T-C		not specified	Likely benign (Nov 18, 2022)
7-27108423-C-T		not specified	Uncertain significance (May 09, 2023)
7-27108438-G-T		not specified	Uncertain significance (Aug 14, 2023)
7-27108465-C-T		not specified	Uncertain significance (Jan 30, 2024)
7-27108571-T-C		not specified	Uncertain significance (May 23, 2023)
7-27108610-T-G		not specified	Uncertain significance (Jan 23, 2024)
7-27108615-T-A		not specified	Uncertain significance (Dec 31, 2023)
7-27108678-G-C		not specified	Uncertain significance (Dec 01, 2022)
7-27110196-G-A		not specified	Uncertain significance (Nov 15, 2021)
7-27110211-G-A		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXA3	protein_coding	protein_coding	ENST00000396352	2	46398

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.945	0.0555	125742	0	4	125746	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.281	264	277	0.952	0.0000167	2811
Missense in Polyphen		42	43.474	0.96609		389
Synonymous	0.0521	134	135	0.994	0.00000947	963
Loss of Function	3.16	1	13.5	0.0739	6.74e-7	141

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)	0.0000365	0.0000352
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.
• Pathway: Activation of anterior HOX genes in hindbrain development during early embryogenesis (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.179
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.563
• hipred: Y
• hipred_score: 0.785
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.414

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxa3
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; muscle phenotype; craniofacial 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; embryo phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail 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); digestive/alimentary phenotype

Gene ontology

• Biological process: angiogenesis;blood vessel remodeling;calcium ion transport;positive regulation of cell population proliferation;anterior/posterior pattern specification;specification of animal organ position;gene expression;magnesium ion homeostasis;glossopharyngeal nerve morphogenesis;bone mineralization;thyroid gland development;positive regulation of transcription by RNA polymerase II;thymus development;animal organ formation;embryonic skeletal system morphogenesis;cartilage development;negative regulation of calcium ion transport;phosphate ion homeostasis;calcium ion homeostasis;parathyroid gland development;positive regulation of receptor binding
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;HMG box domain binding