HOXA9

homeobox A9, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 7:27162438-27175180

Previous symbols: [ "HOX1G", "HOX1" ]

Links

ENSG00000078399 ∙ NCBI:3205 ∙ OMIM:142956 ∙ HGNC:5109 ∙ Uniprot:P31269 ∙ 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 HOXA9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXA9 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			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	1

Variants in HOXA9

This is a list of pathogenic ClinVar variants found in the HOXA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-27163636-C-G		not specified	Uncertain significance (Oct 20, 2021)
7-27163650-T-A		not specified	Uncertain significance (Dec 21, 2023)
7-27163700-C-A		not specified	Uncertain significance (Jan 22, 2024)
7-27163709-T-G		not specified	Uncertain significance (Jul 06, 2021)
7-27163754-T-G			Uncertain significance (Nov 01, 2016)
7-27163782-T-G		not specified	Uncertain significance (Dec 15, 2023)
7-27163795-C-T			Benign (Jun 01, 2018)
7-27163821-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-27163840-A-T		not specified	Uncertain significance (Oct 26, 2022)
7-27164893-G-T		not specified	Uncertain significance (Jul 20, 2021)
7-27164907-C-G		not specified	Uncertain significance (Dec 27, 2023)
7-27164907-C-T		not specified	Uncertain significance (May 31, 2023)
7-27164937-G-A		not specified	Uncertain significance (Sep 25, 2023)
7-27164988-T-C		not specified	Uncertain significance (Sep 15, 2021)
7-27165045-G-A		not specified	Uncertain significance (Jun 07, 2023)
7-27165099-G-T		not specified	Uncertain significance (Jun 02, 2023)
7-27165112-G-T		not specified	Uncertain significance (Aug 12, 2021)
7-27165130-A-G		not specified	Uncertain significance (Jan 17, 2024)
7-27165154-C-G		Hand-foot-genital syndrome	Uncertain significance (-)
7-27165162-G-A		not specified	Uncertain significance (Jan 19, 2022)
7-27165169-G-A		not specified	Uncertain significance (Mar 29, 2022)
7-27165265-C-T		not specified	Uncertain significance (Sep 28, 2022)
7-27165273-A-C		not specified	Uncertain significance (Jun 05, 2023)
7-27165288-T-C		not specified	Uncertain significance (Nov 20, 2023)
7-27165316-G-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXA9	protein_coding	protein_coding	ENST00000343483	2	8064

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000436	0.419	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0583	157	155	1.01	0.00000755	1743
Missense in Polyphen		67	79.748	0.84015		878
Synonymous	-2.68	94	66.3	1.42	0.00000331	554
Loss of Function	0.295	7	7.90	0.887	3.81e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000798	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000997	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. Required for induction of E-selectin and VCAM-1, on the endothelial cells surface at sites of inflammation. {ECO:0000269|PubMed:22269951}.
• Disease: DISEASE: Note=A chromosomal aberration involving HOXA9 is found in a form of acute myeloid leukemia. Translocation t(7;11)(p15;p15) with NUP98.; DISEASE: Note=A chromosomal aberration involving HOXA9 may contribute to disease progression in chronic myeloid leukemia. Translocation t(7;17)(p15;q23) with MSI2.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);TGF_beta_Receptor (Consensus)

Recessive Scores

• pRec: 0.406

Intolerance Scores

• loftool: 0.212
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.941
• hipred: N
• hipred_score: 0.372
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.822

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxa9
• Phenotype: immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype; reproductive system phenotype; hematopoietic system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: transcription, DNA-templated;multicellular organism development;spermatogenesis;single fertilization;male gonad development;anterior/posterior pattern specification;proximal/distal pattern formation;mammary gland development;embryonic forelimb morphogenesis;endothelial cell activation;negative regulation of myeloid cell differentiation;positive regulation of transcription by RNA polymerase II;embryonic skeletal system development;uterus development;definitive hemopoiesis
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;enzyme binding