COMMD7

COMM domain containing 7, the group of CCC complex|COMM domain containing

Basic information

Region (hg38): 20:32702698-32743467

Previous symbols: [ "C20orf92" ]

Links

ENSG00000149600 ∙ NCBI:149951 ∙ OMIM:616703 ∙ HGNC:16223 ∙ Uniprot:Q86VX2 ∙ 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 COMMD7 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COMMD7 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	12	0	0

Variants in COMMD7

This is a list of pathogenic ClinVar variants found in the COMMD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-32703447-G-A		not specified	Uncertain significance (Dec 28, 2022)
20-32704020-C-T			Benign (Jul 26, 2018)
20-32704038-C-T		not specified	Uncertain significance (Mar 29, 2022)
20-32704046-T-C		not specified	Uncertain significance (Feb 15, 2023)
20-32704049-C-A		not specified	Uncertain significance (Jun 29, 2022)
20-32704445-A-C		not specified	Uncertain significance (Apr 12, 2023)
20-32704879-G-A		not specified	Uncertain significance (Sep 13, 2023)
20-32704898-G-T		not specified	Uncertain significance (Dec 15, 2023)
20-32706600-T-C		not specified	Uncertain significance (Apr 06, 2022)
20-32706721-G-A		not specified	Uncertain significance (Jul 29, 2022)
20-32727938-C-A		not specified	Uncertain significance (Mar 28, 2023)
20-32727958-G-A		not specified	Uncertain significance (Jan 06, 2023)
20-32728099-T-C		not specified	Uncertain significance (Jun 02, 2023)
20-32728106-G-C		not specified	Uncertain significance (Dec 28, 2022)
20-32728132-G-T		not specified	Uncertain significance (Oct 03, 2023)
20-32743321-T-C		not specified	Uncertain significance (Dec 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COMMD7	protein_coding	protein_coding	ENST00000278980	9	41311

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.75e-8	0.324	124769	0	25	124794	0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.587	84	101	0.835	0.00000476	1311
Missense in Polyphen		19	24.751	0.76766		368
Synonymous	0.321	34	36.5	0.932	0.00000199	355
Loss of Function	0.565	12	14.3	0.839	6.73e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000115	0.000115
Middle Eastern	0.000167	0.000167
South Asian	0.000166	0.000163
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate activity of cullin-RING E3 ubiquitin ligase (CRL) complexes (PubMed:21778237). Associates with the NF-kappa-B complex and suppresses its transcriptional activity (PubMed:15799966). {ECO:0000269|PubMed:15799966, ECO:0000305|PubMed:21778237}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.790
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.0738
• hipred: N
• hipred_score: 0.251
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Commd7

Gene ontology

• Biological process: negative regulation of NF-kappaB transcription factor activity;tumor necrosis factor-mediated signaling pathway;negative regulation of transcription, DNA-templated
• Cellular component: cytoplasmic vesicle;intracellular membrane-bounded organelle
• Molecular function: protein binding;NF-kappaB binding