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.

not_specified (33 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000153633.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			33 clinvar			33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	2	0

Loading clinvar variants...

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