HOXC6

homeobox C6, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 12:53990623-54030823

Previous symbols: [ "HOX3C", "HOX3" ]

Links

ENSG00000197757 ∙ NCBI:3223 ∙ OMIM:142972 ∙ HGNC:5128 ∙ Uniprot:P09630 ∙ 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 HOXC6 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXC6 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	6	0	0

Variants in HOXC6

This is a list of pathogenic ClinVar variants found in the HOXC6 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54000204-C-T		not specified	Uncertain significance (Aug 20, 2023)
12-54000243-G-A		not specified	Uncertain significance (Jul 12, 2022)
12-54000267-A-G		not specified	Uncertain significance (Sep 16, 2021)
12-54000465-A-C		not specified	Uncertain significance (Feb 17, 2024)
12-54000490-C-G		not specified	Uncertain significance (Nov 21, 2023)
12-54000553-C-T			Benign (Jun 14, 2018)
12-54000577-G-T		not specified	Uncertain significance (Mar 14, 2023)
12-54000601-A-C		not specified	Uncertain significance (Jul 09, 2021)
12-54000613-T-A		not specified	Uncertain significance (Jul 27, 2022)
12-54000613-T-G		not specified	Uncertain significance (Dec 14, 2023)
12-54002432-A-C		not specified	Uncertain significance (Dec 28, 2023)
12-54002460-G-A		not specified	Uncertain significance (Sep 12, 2023)
12-54002552-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-54002591-C-T		not specified	Uncertain significance (May 03, 2023)
12-54009330-G-A		not specified	Uncertain significance (Mar 13, 2023)
12-54009363-C-G		not specified	Uncertain significance (Apr 04, 2023)
12-54009364-G-T		not specified	Uncertain significance (Feb 27, 2023)
12-54009399-G-C		not specified	Uncertain significance (Feb 23, 2023)
12-54009415-G-T		not specified	Uncertain significance (Nov 22, 2022)
12-54009517-C-G		not specified	Uncertain significance (Jan 29, 2024)
12-54009588-G-T		not specified	Uncertain significance (Oct 20, 2023)
12-54009616-A-C		not specified	Uncertain significance (Dec 07, 2021)
12-54009618-C-G		not specified	Uncertain significance (Sep 13, 2023)
12-54009669-T-G		not specified	Uncertain significance (Feb 05, 2024)
12-54011340-G-A		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXC6	protein_coding	protein_coding	ENST00000243108	2	40200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.512	0.485	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.973	107	139	0.768	0.00000680	1526
Missense in Polyphen		38	65.229	0.58256		709
Synonymous	0.531	55	60.2	0.913	0.00000290	466
Loss of Function	2.43	2	10.5	0.190	4.92e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	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: 0.124

Intolerance Scores

• loftool: 0.102
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.895
• hipred: Y
• hipred_score: 0.837
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxc6
• Phenotype: endocrine/exocrine gland 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); skeleton phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;anterior/posterior pattern specification;positive regulation of transcription by RNA polymerase II;embryonic skeletal system development;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;transcription corepressor activity