COMMD10

COMM domain containing 10, the group of COMM domain containing|CCC complex

Basic information

Region (hg38): 5:116085015-116412762

Links

ENSG00000145781 ∙ NCBI:51397 ∙ OMIM:616704 ∙ HGNC:30201 ∙ Uniprot:Q9Y6G5 ∙ 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 COMMD10 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COMMD10 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			7	2		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in COMMD10

This is a list of pathogenic ClinVar variants found in the COMMD10 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-116085062-C-T		not specified	Likely benign (Dec 12, 2022)
5-116087499-T-C		not specified	Uncertain significance (Mar 06, 2023)
5-116087531-G-C		not specified	Uncertain significance (Aug 10, 2021)
5-116087561-C-T		not specified	Uncertain significance (Dec 21, 2022)
5-116091122-C-T		not specified	Likely benign (Dec 07, 2021)
5-116092674-C-T		not specified	Uncertain significance (May 17, 2023)
5-116134166-T-A		not specified	Uncertain significance (Feb 22, 2023)
5-116291562-G-T		not specified	Uncertain significance (Feb 15, 2023)
5-116291568-T-C		not specified	Uncertain significance (Feb 23, 2023)
5-116292455-A-G		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COMMD10	protein_coding	protein_coding	ENST00000274458	7	327772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.48e-12	0.00937	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.880	127	102	1.25	0.00000516	1314
Missense in Polyphen		34	27.943	1.2168		370
Synonymous	-1.40	47	36.3	1.30	0.00000180	370
Loss of Function	-1.02	15	11.3	1.33	4.78e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000407	0.000406
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000446	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000153	0.000141
Middle Eastern	0.000446	0.000435
South Asian	0.000210	0.000196
Other	0.000179	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate activity of cullin-RING E3 ubiquitin ligase (CRL) complexes (PubMed:21778237). May down-regulate activation of NF-kappa-B (PubMed:15799966). {ECO:0000269|PubMed:15799966, ECO:0000305|PubMed:21778237}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.806
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.245
• hipred: N
• hipred_score: 0.204
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Commd10
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); normal phenotype; neoplasm; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding