HOXC11

homeobox C11, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 12:53973126-53977643

Previous symbols: [ "HOX3H" ]

Links

ENSG00000123388 ∙ NCBI:3227 ∙ OMIM:605559 ∙ HGNC:5123 ∙ Uniprot:O43248 ∙ 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 HOXC11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXC11 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in HOXC11

This is a list of pathogenic ClinVar variants found in the HOXC11 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53973311-G-C		not specified	Uncertain significance (Dec 08, 2023)
12-53973334-C-A		not specified	Uncertain significance (Jan 30, 2024)
12-53973339-A-G		not specified	Uncertain significance (Mar 25, 2024)
12-53973432-C-T		not specified	Uncertain significance (Apr 17, 2023)
12-53973449-G-A		not specified	Uncertain significance (Feb 27, 2024)
12-53973519-A-G		not specified	Uncertain significance (May 17, 2023)
12-53973600-C-T		not specified	Uncertain significance (Jan 17, 2024)
12-53973615-A-G		not specified	Uncertain significance (Sep 25, 2023)
12-53973617-C-A		not specified	Uncertain significance (Jun 30, 2023)
12-53973645-C-G		not specified	Uncertain significance (Oct 26, 2022)
12-53973647-G-T		not specified	Uncertain significance (Dec 28, 2022)
12-53973728-G-C		not specified	Uncertain significance (Nov 10, 2022)
12-53973743-G-A		not specified	Uncertain significance (Feb 06, 2023)
12-53973764-G-A		not specified	Uncertain significance (Nov 12, 2021)
12-53973782-C-T		not specified	Uncertain significance (Dec 20, 2022)
12-53973810-C-G		not specified	Likely benign (Jun 11, 2021)
12-53973815-C-G		not specified	Uncertain significance (Jul 09, 2021)
12-53975224-C-G		not specified	Uncertain significance (Aug 16, 2021)
12-53975232-G-C		not specified	Uncertain significance (Aug 13, 2021)
12-53975263-G-C			Likely benign (Jan 01, 2023)
12-53975271-A-G		not specified	Uncertain significance (Jan 03, 2022)
12-53975394-C-G		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXC11	protein_coding	protein_coding	ENST00000546378	2	4518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00406	0.871	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.134	167	162	1.03	0.00000742	1932
Missense in Polyphen		72	73.557	0.97884		894
Synonymous	-0.415	78	73.5	1.06	0.00000357	634
Loss of Function	1.29	5	9.24	0.541	3.98e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
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. Binds to a promoter element of the lactase-phlorizin hydrolase gene.
• Pathway: Endoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.739
• hipred: Y
• hipred_score: 0.684
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxc11
• Phenotype: reproductive system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype; cellular phenotype

Gene ontology

• Biological process: metanephros development;organ induction;endoderm development;anterior/posterior pattern specification;proximal/distal pattern formation;embryonic digit morphogenesis;positive regulation of transcription by RNA polymerase II;embryonic skeletal joint morphogenesis
• Cellular component: nucleoplasm;cytosol
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific