HOXC9

homeobox C9, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 12:53994895-54003337

Previous symbols: [ "HOX3", "HOX3B" ]

Links

ENSG00000180806

∙ NCBI:3225 ∙ OMIM:142971 ∙ HGNC:5130 ∙ Uniprot:P31274 ∙ 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 HOXC9 gene.

not_specified (31 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXC9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006897.3. 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						0
missense			31 clinvar		1 clinvar	32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXC9	protein_coding	protein_coding	ENST00000303450	2	8443

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0130	0.870	125736	0	8	125744	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.354	142	154	0.920	0.00000766	1674
Missense in Polyphen		58	69.702	0.83211		735
Synonymous	-1.18	80	67.7	1.18	0.00000348	515
Loss of Function	1.30	4	7.95	0.503	3.83e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000767	0.0000462
European (Non-Finnish)	0.0000360	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	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: Differentiation of white and brown adipocyte (Consensus)

Recessive Scores

pRec: 0.128

Haploinsufficiency Scores

pHI: 0.578
hipred: Y
hipred_score: 0.674
ghis: 0.518

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.882

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Hoxc9
Phenotype: growth/size/body region phenotype; skeleton phenotype; limbs/digits/tail phenotype;

Zebrafish Information Network

Gene name: hoxc9a
Affected structure: vascular lymphangioblast
Phenotype tag: abnormal
Phenotype quality: hypoplastic

Gene ontology

Biological process: transcription, DNA-templated;regulation of transcription by RNA polymerase II;anterior/posterior pattern specification;embryonic skeletal system morphogenesis
Cellular component: nucleoplasm;aggresome
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding