HOXC9

homeobox C9, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 12:53994894-54003337

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.

• Inborn genetic diseases (9 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.

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						0
missense			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	1

Variants in HOXC9

This is a list of pathogenic ClinVar variants found in the HOXC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54000204-C-T		not specified	Uncertain significance (Aug 20, 2023)
12-54000243-G-A		not specified	Uncertain significance (Jul 12, 2022)
12-54000267-A-G		not specified	Uncertain significance (Sep 16, 2021)
12-54000465-A-C		not specified	Uncertain significance (Feb 17, 2024)
12-54000490-C-G		not specified	Uncertain significance (Nov 21, 2023)
12-54000553-C-T			Benign (Jun 14, 2018)
12-54000577-G-T		not specified	Uncertain significance (Mar 14, 2023)
12-54000601-A-C		not specified	Uncertain significance (Jul 09, 2021)
12-54000613-T-A		not specified	Uncertain significance (Jul 27, 2022)
12-54000613-T-G		not specified	Uncertain significance (Dec 14, 2023)
12-54002432-A-C		not specified	Uncertain significance (Dec 28, 2023)
12-54002460-G-A		not specified	Uncertain significance (Sep 12, 2023)
12-54002552-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-54002591-C-T		not specified	Uncertain significance (May 03, 2023)

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