HOXC10

homeobox C10, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 12:53985065-53990279

Previous symbols: [ "HOX3I" ]

Links

ENSG00000180818 ∙ NCBI:3226 ∙ OMIM:605560 ∙ HGNC:5122 ∙ Uniprot:Q9NYD6 ∙ 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 HOXC10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXC10 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	1

Variants in HOXC10

This is a list of pathogenic ClinVar variants found in the HOXC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53985377-A-T		not specified	Uncertain significance (Dec 24, 2024)
12-53985386-G-A		not specified	Uncertain significance (Feb 07, 2025)
12-53985401-G-A		not specified	Uncertain significance (Mar 17, 2023)
12-53985426-G-T		not specified	Uncertain significance (Aug 09, 2021)
12-53985452-G-A		not specified	Uncertain significance (Oct 26, 2021)
12-53985506-A-C		not specified	Uncertain significance (Aug 12, 2021)
12-53985511-C-T			Benign (Dec 31, 2019)
12-53985512-G-T		not specified	Uncertain significance (Dec 14, 2022)
12-53985518-C-A		not specified	Uncertain significance (Sep 26, 2023)
12-53985552-C-T		not specified	Uncertain significance (Feb 08, 2025)
12-53985618-C-A		not specified	Uncertain significance (Jun 24, 2022)
12-53985675-G-C		not specified	Uncertain significance (May 02, 2023)
12-53985677-G-C		not specified	Uncertain significance (May 13, 2024)
12-53985717-C-A		not specified	Uncertain significance (Jan 07, 2025)
12-53985719-A-T		not specified	Uncertain significance (Apr 24, 2024)
12-53985726-C-G		not specified	Uncertain significance (Sep 11, 2024)
12-53985781-C-A		not specified	Uncertain significance (Aug 03, 2022)
12-53985816-A-G		not specified	Uncertain significance (Sep 30, 2024)
12-53985843-A-C		not specified	Uncertain significance (Jan 07, 2025)
12-53985864-C-T		not specified	Uncertain significance (Dec 22, 2023)
12-53985924-G-T		not specified	Uncertain significance (Dec 18, 2023)
12-53985956-G-C		not specified	Uncertain significance (Dec 28, 2022)
12-53985984-C-T		not specified	Uncertain significance (May 25, 2022)
12-53989174-A-C		not specified	Uncertain significance (Jun 29, 2023)
12-53989256-C-G		not specified	Uncertain significance (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXC10	protein_coding	protein_coding	ENST00000303460	2	5215

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.174	0.814	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.216	194	203	0.957	0.00000963	2248
Missense in Polyphen		32	36.38	0.8796		438
Synonymous	-0.480	94	88.3	1.06	0.00000452	678
Loss of Function	2.17	3	10.6	0.282	4.51e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

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: 0.218
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.650
• hipred: Y
• hipred_score: 0.587
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.436

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxc10
• Phenotype: growth/size/body region phenotype; muscle phenotype; limbs/digits/tail 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; 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)

Gene ontology

• Biological process: skeletal system development;positive regulation of cell population proliferation;anterior/posterior pattern specification;proximal/distal pattern formation;spinal cord motor neuron cell fate specification;embryonic limb morphogenesis;positive regulation of transcription by RNA polymerase II;neuromuscular process;negative regulation of cold-induced thermogenesis
• Cellular component: nucleoplasm;nuclear body
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific