HOXC5

homeobox C5, the group of HOXL subclass homeoboxes|MicroRNA protein coding host genes

Basic information

Region (hg38): 12:54033050-54035361

Previous symbols: [ "HOX3D", "HOX3" ]

Links

ENSG00000172789 ∙ NCBI:3222 ∙ OMIM:142973 ∙ HGNC:5127 ∙ Uniprot:Q00444 ∙ 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 HOXC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXC5 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			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	2

Variants in HOXC5

This is a list of pathogenic ClinVar variants found in the HOXC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54033150-T-C		not specified	Uncertain significance (Jan 16, 2024)
12-54033155-G-C			Benign (Jul 26, 2018)
12-54033171-C-A		not specified	Uncertain significance (Oct 13, 2023)
12-54033183-A-G		not specified	Uncertain significance (Mar 31, 2024)
12-54033195-G-A		not specified	Uncertain significance (Jul 19, 2023)
12-54033243-G-A		not specified	Uncertain significance (Apr 19, 2024)
12-54033307-A-C		not specified	Uncertain significance (Oct 29, 2024)
12-54033359-G-A			Benign (Jul 26, 2018)
12-54033388-A-G		not specified	Uncertain significance (Jan 09, 2024)
12-54033397-C-T		not specified	Uncertain significance (Aug 12, 2021)
12-54033405-A-G		not specified	Uncertain significance (May 02, 2024)
12-54033412-G-T		not specified	Uncertain significance (Dec 22, 2023)
12-54033417-T-A		not specified	Uncertain significance (May 16, 2022)
12-54033433-C-T		not specified	Uncertain significance (Nov 15, 2024)
12-54033525-C-A		not specified	Uncertain significance (Aug 14, 2023)
12-54033549-T-A		not specified	Uncertain significance (Dec 17, 2023)
12-54034281-C-G		not specified	Uncertain significance (Jul 30, 2024)
12-54034356-G-A		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXC5	protein_coding	protein_coding	ENST00000312492	2	2506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000578	0.475	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.578	146	128	1.14	0.00000595	1437
Missense in Polyphen		48	37.475	1.2809		469
Synonymous	0.139	50	51.3	0.975	0.00000236	422
Loss of Function	0.422	7	8.31	0.842	3.58e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000486	0.000485
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000602	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000201	0.000193
Middle Eastern	0.0000602	0.0000544
South Asian	0.000392	0.000392
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.

Intolerance Scores

• loftool: 0.377
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.881
• hipred: N
• hipred_score: 0.170
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.760

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxc5
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;anterior/posterior pattern specification;positive regulation of transcription by RNA polymerase II;embryonic skeletal system development
• Cellular component: nucleus;nucleoplasm;cell junction
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity