HOXD12

homeobox D12, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 2:176099795-176102489

Previous symbols: [ "HOX4H" ]

Links

ENSG00000170178 ∙ NCBI:3238 ∙ OMIM:142988 ∙ HGNC:5135 ∙ Uniprot:P35452 ∙ 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 HOXD12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXD12 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			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	0	0

Variants in HOXD12

This is a list of pathogenic ClinVar variants found in the HOXD12 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-176099805-T-C		not specified	Uncertain significance (Feb 09, 2025)
2-176099809-A-G		not specified	Uncertain significance (Oct 20, 2024)
2-176099862-C-T		not specified	Uncertain significance (Dec 14, 2023)
2-176099863-C-T		not specified	Uncertain significance (Nov 27, 2024)
2-176099961-A-G		not specified	Uncertain significance (Sep 22, 2022)
2-176099977-C-T		not specified	Uncertain significance (Jul 19, 2023)
2-176099992-C-A		not specified	Uncertain significance (Jun 07, 2024)
2-176099998-C-T		not specified	Uncertain significance (Dec 05, 2024)
2-176100024-C-A		HOXD12-related disorder	Likely benign (Apr 07, 2022)
2-176100052-G-A		not specified	Uncertain significance (Feb 24, 2025)
2-176100105-G-C		not specified • HOXD12-related disorder	Uncertain significance (Aug 08, 2022)
2-176100130-A-C		not specified	Uncertain significance (Feb 27, 2024)
2-176100136-G-A		not specified	Uncertain significance (Aug 01, 2024)
2-176100141-C-A		not specified	Uncertain significance (Aug 12, 2021)
2-176100148-G-T		not specified	Uncertain significance (Apr 19, 2024)
2-176100153-T-C		not specified	Likely benign (Jan 29, 2025)
2-176100216-T-C		not specified	Uncertain significance (Aug 04, 2023)
2-176100232-G-A		not specified	Uncertain significance (Sep 22, 2022)
2-176100241-C-T		not specified	Uncertain significance (Jul 13, 2021)
2-176100259-T-C		not specified	Uncertain significance (Dec 10, 2024)
2-176100264-G-T		not specified	Uncertain significance (Apr 27, 2023)
2-176100283-G-A		not specified	Uncertain significance (Feb 25, 2025)
2-176100298-C-A		not specified	Uncertain significance (Dec 27, 2022)
2-176100300-A-G		not specified	Uncertain significance (Jun 11, 2024)
2-176100310-T-C		not specified	Uncertain significance (Dec 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXD12	protein_coding	protein_coding	ENST00000406506	2	1951

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000277	0.571	124564	0	59	124623	0.000237

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.34	202	155	1.30	0.00000713	1675
Missense in Polyphen		78	54.902	1.4207		674
Synonymous	-0.918	81	71.1	1.14	0.00000335	587
Loss of Function	0.538	6	7.60	0.789	3.24e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000355	0.000319
Ashkenazi Jewish	0.00	0.00
East Asian	0.000317	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.000400	0.000345
Middle Eastern	0.000317	0.000278
South Asian	0.000277	0.000229
Other	0.000187	0.000165

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: 0.193

Intolerance Scores

• loftool: 0.432
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.15

Haploinsufficiency Scores

• pHI: 0.889
• hipred: N
• hipred_score: 0.318
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.750

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxd12
• Phenotype: digestive/alimentary phenotype; limbs/digits/tail phenotype; skeleton phenotype; reproductive system phenotype; muscle phenotype

Gene ontology

• Biological process: skeletal system development;regulation of transcription by RNA polymerase II;pattern specification process;embryonic digit morphogenesis
• Cellular component: nucleus;transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding