HOXC4

homeobox C4, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 12:54016931-54056030

Previous symbols: [ "HOX3", "HOX3E" ]

Links

ENSG00000198353 ∙ NCBI:3221 ∙ OMIM:142974 ∙ HGNC:5126 ∙ Uniprot:P09017 ∙ 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 HOXC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXC4 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			20		2	22
Total	0	0	31	2	2

Variants in HOXC4

This is a list of pathogenic ClinVar variants found in the HOXC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54028565-C-T		not specified	Uncertain significance (Apr 19, 2024)
12-54028589-A-G		not specified	Uncertain significance (Nov 19, 2024)
12-54028600-A-C		not specified	Uncertain significance (May 25, 2022)
12-54028649-C-T		not specified	Uncertain significance (Jan 24, 2024)
12-54028705-G-A		not specified	Uncertain significance (Aug 13, 2021)
12-54028769-T-C		not specified	Uncertain significance (Feb 28, 2024)
12-54028780-T-A		not specified	Uncertain significance (Jan 10, 2023)
12-54028819-A-G		not specified	Uncertain significance (Aug 27, 2024)
12-54028840-G-C		not specified	Uncertain significance (Feb 05, 2024)
12-54029840-T-A		not specified	Uncertain significance (Oct 03, 2022)
12-54029865-C-T		not specified	Uncertain significance (Oct 29, 2021)
12-54029874-C-G		not specified	Uncertain significance (Dec 04, 2024)
12-54029879-G-A		not specified	Uncertain significance (Sep 25, 2024)
12-54029933-G-A		not specified	Uncertain significance (Oct 30, 2023)
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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXC4	protein_coding	protein_coding	ENST00000609810	2	39099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.168	0.819	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.633	133	155	0.857	0.00000728	1703
Missense in Polyphen		24	53.175	0.45134		620
Synonymous	0.352	65	68.7	0.946	0.00000348	519
Loss of Function	2.15	3	10.6	0.284	4.60e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.000110	0.000109
South Asian	0.00	0.00
Other	0.000336	0.000326

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: Activation of anterior HOX genes in hindbrain development during early embryogenesis (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.162
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.246
• hipred: Y
• hipred_score: 0.761
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxc4
• Phenotype: muscle phenotype; hematopoietic system phenotype; 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); immune system phenotype; skeleton phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: skeletal system development;anterior/posterior pattern specification;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;cartilage development
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;activating transcription factor binding;HMG box domain binding