HOXC12

homeobox C12, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 12:53954903-53958956

Previous symbols: [ "HOX3", "HOX3F", "HOC3F" ]

Links

ENSG00000123407 ∙ NCBI:3228 ∙ OMIM:142975 ∙ HGNC:5124 ∙ Uniprot:P31275 ∙ 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 HOXC12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXC12 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				2		2
missense			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	3	0

Variants in HOXC12

This is a list of pathogenic ClinVar variants found in the HOXC12 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53954949-T-C		not specified	Uncertain significance (Feb 12, 2025)
12-53954951-A-C		not specified	Uncertain significance (Jan 10, 2023)
12-53955029-G-T		not specified	Uncertain significance (Jul 31, 2024)
12-53955066-G-T		not specified	Uncertain significance (Jul 12, 2023)
12-53955095-C-A		not specified	Uncertain significance (Jul 06, 2021)
12-53955099-C-T		not specified	Uncertain significance (Jan 10, 2025)
12-53955102-C-T		not specified	Uncertain significance (Mar 06, 2025)
12-53955127-G-A			Likely benign (Sep 01, 2022)
12-53955129-C-G		not specified	Uncertain significance (Nov 13, 2024)
12-53955174-C-G		not specified	Uncertain significance (May 14, 2025)
12-53955197-G-T		not specified	Uncertain significance (Jun 23, 2023)
12-53955225-G-A		not specified	Uncertain significance (May 16, 2025)
12-53955276-C-T		not specified	Uncertain significance (Mar 01, 2023)
12-53955329-G-C		not specified	Uncertain significance (Jul 26, 2022)
12-53955457-C-G			Likely benign (Sep 01, 2022)
12-53955466-C-A		not specified	Uncertain significance (Jan 08, 2024)
12-53955500-G-C		not specified	Uncertain significance (Jun 24, 2022)
12-53955513-A-T		not specified	Uncertain significance (May 06, 2025)
12-53955533-G-A		not specified	Uncertain significance (Mar 20, 2023)
12-53955537-G-A		not specified	Uncertain significance (Feb 21, 2024)
12-53956353-C-A		not specified	Uncertain significance (Aug 11, 2024)
12-53956375-C-T		not specified	Uncertain significance (Nov 14, 2024)
12-53956439-G-T		not specified	Uncertain significance (Jun 24, 2022)
12-53956508-A-G		not specified	Uncertain significance (Feb 08, 2025)
12-53956511-G-A		not specified	Uncertain significance (Jan 29, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXC12	protein_coding	protein_coding	ENST00000243103	2	4123

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.43e-9	0.0222	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.287	151	141	1.07	0.00000680	1758
Missense in Polyphen		62	66.709	0.92941		806
Synonymous	-1.85	86	66.8	1.29	0.00000325	623
Loss of Function	-1.31	11	7.19	1.53	3.08e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000118	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000368	0.0000327
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.

Recessive Scores

• pRec: 0.111

Haploinsufficiency Scores

• pHI: 0.481
• hipred: Y
• hipred_score: 0.526
• ghis: 0.483

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: Hoxc12
• Phenotype: limbs/digits/tail phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding