HOXD9

homeobox D9, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 2:176122718-176124937

Previous symbols: [ "HOX4C", "HOX4" ]

Links

ENSG00000128709 ∙ NCBI:3235 ∙ OMIM:142982 ∙ HGNC:5140 ∙ Uniprot:P28356 ∙ 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 HOXD9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXD9 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			21	3	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	2

Variants in HOXD9

This is a list of pathogenic ClinVar variants found in the HOXD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-176122788-G-A		not specified	Uncertain significance (Aug 12, 2021)
2-176122788-G-C			Benign (Jul 15, 2018)
2-176122875-C-A		not specified	Uncertain significance (Dec 19, 2023)
2-176122935-C-T		not specified	Uncertain significance (Jun 17, 2024)
2-176122952-G-C		not specified	Uncertain significance (Jun 08, 2022)
2-176122964-T-C		not specified	Uncertain significance (Feb 07, 2023)
2-176123067-T-G		not specified	Uncertain significance (Apr 07, 2022)
2-176123102-C-A		HOXD9-related disorder	Likely benign (Aug 09, 2022)
2-176123121-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-176123186-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-176123226-C-G		not specified	Uncertain significance (Jun 01, 2023)
2-176123231-G-C		HOXD9-related disorder	Likely benign (Mar 20, 2023)
2-176123231-G-T		HOXD9-related disorder	Likely benign (Feb 28, 2023)
2-176123234-C-A		not specified	Uncertain significance (Nov 30, 2021)
2-176123312-A-G		not specified	Uncertain significance (Dec 19, 2023)
2-176123358-G-A		not specified	Uncertain significance (Apr 12, 2024)
2-176123418-C-A		not specified	Uncertain significance (Sep 27, 2022)
2-176123435-G-A		not specified	Uncertain significance (Jan 22, 2024)
2-176123441-G-C		not specified	Uncertain significance (Sep 17, 2021)
2-176123487-C-T		not specified	Uncertain significance (Apr 18, 2023)
2-176123509-C-G		not specified	Uncertain significance (Jun 09, 2022)
2-176123573-C-G		not specified	Uncertain significance (Feb 28, 2023)
2-176123955-T-G		not specified	Uncertain significance (Dec 06, 2021)
2-176123994-C-G		not specified	Uncertain significance (Dec 21, 2023)
2-176124037-C-T			Benign (Jul 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXD9	protein_coding	protein_coding	ENST00000249499	2	2766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0170	0.898	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.578	147	168	0.875	0.00000781	2187
Missense in Polyphen		49	60.999	0.8033		749
Synonymous	-0.973	82	71.5	1.15	0.00000364	751
Loss of Function	1.45	4	8.58	0.466	3.72e-7	107

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)	0.0000461	0.0000439
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.

Haploinsufficiency Scores

• pHI: 0.481
• hipred: Y
• hipred_score: 0.510
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.883

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxd9
• Phenotype: cellular phenotype; muscle 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); endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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); reproductive system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription, DNA-templated;single fertilization;skeletal muscle tissue development;adult locomotory behavior;anterior/posterior pattern specification;proximal/distal pattern formation;mammary gland development;embryonic forelimb morphogenesis;hindlimb morphogenesis;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;peripheral nervous system neuron development
• Cellular component: nucleus;nucleolus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific