COMMD6

COMM domain containing 6, the group of CCC complex|COMM domain containing

Basic information

Region (hg38): 13:75525214-75549439

Links

ENSG00000188243

∙ NCBI:170622 ∙ OMIM:612377 ∙ HGNC:24015 ∙ Uniprot:Q7Z4G1 ∙ 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 COMMD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COMMD6 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			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in COMMD6

This is a list of pathogenic ClinVar variants found in the COMMD6 region.

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

Position	Phenotype	Significance	ClinVar
13-75530139-A-G	not specified	Uncertain significance (Aug 26, 2024)	3495903
13-75530150-C-G	not specified	Uncertain significance (Feb 17, 2022)	2348804
13-75530224-C-T	not specified	Uncertain significance (Feb 09, 2025)	2225942
13-75530239-T-C	not specified	Uncertain significance (Feb 22, 2025)	3835513

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COMMD6	protein_coding	protein_coding	ENST00000355801	5	24226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.172	0.775	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.687	65	51.2	1.27	0.00000248	634
Missense in Polyphen		6	2.4011	2.4988		24
Synonymous	-0.743	24	19.8	1.21	0.00000111	179
Loss of Function	1.60	2	6.35	0.315	2.69e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: May modulate activity of cullin-RING E3 ubiquitin ligase (CRL) complexes (PubMed:21778237). Down-regulates activation of NF-kappa-B. Inhibits TNF-induced NFKB1 activation. {ECO:0000269|PubMed:15799966, ECO:0000269|PubMed:16573520, ECO:0000305|PubMed:21778237}.;
Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

pRec: 0.101

Intolerance Scores

loftool: 0.759
rvis_EVS: 0.21
rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

pHI: 0.380
hipred: Y
hipred_score: 0.623
ghis: 0.499

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0978

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Commd6
Phenotype

Gene ontology

Biological process: negative regulation of NF-kappaB transcription factor activity
Cellular component: nucleus;cytoplasm
Molecular function: protein binding;NF-kappaB binding