HOXC8

homeobox C8, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 12:54008984-54012769

Previous symbols: [ "HOX3", "HOX3A" ]

Links

ENSG00000037965 ∙ NCBI:3224 ∙ OMIM:142970 ∙ HGNC:5129 ∙ Uniprot:P31273 ∙ 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 HOXC8 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXC8 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in HOXC8

This is a list of pathogenic ClinVar variants found in the HOXC8 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54009330-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
HOXC8	protein_coding	protein_coding	ENST00000040584	2	4739

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.170	0.818	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.502	112	128	0.875	0.00000620	1590
Missense in Polyphen		26	40.151	0.64756		468
Synonymous	-2.61	75	51.2	1.46	0.00000264	446
Loss of Function	2.16	3	10.6	0.284	4.70e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000331	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.
• Pathway: miR-targeted genes in epithelium - TarBase;Differentiation of white and brown adipocyte (Consensus)

Recessive Scores

• pRec: 0.180

Intolerance Scores

• loftool: 0.170
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.428
• hipred: Y
• hipred_score: 0.747
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxc8
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;anterior/posterior pattern specification;neuron differentiation;skeletal system morphogenesis
• Cellular component: nucleoplasm;microtubule cytoskeleton
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding