COMMD4

COMM domain containing 4, the group of CCC complex|COMM domain containing

Basic information

Region (hg38): 15:75336020-75343224

Links

ENSG00000140365 ∙ NCBI:54939 ∙ OMIM:616701 ∙ HGNC:26027 ∙ Uniprot:Q9H0A8 ∙ 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 COMMD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COMMD4 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			20			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	20	0	0

Variants in COMMD4

This is a list of pathogenic ClinVar variants found in the COMMD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-75338081-A-G		not specified	Uncertain significance (Jun 27, 2023)
15-75338097-C-G		not specified	Uncertain significance (Feb 06, 2025)
15-75338120-C-T		not specified	Uncertain significance (Mar 15, 2024)
15-75338397-G-A		not specified	Uncertain significance (Jan 03, 2024)
15-75338410-A-G		not specified	Uncertain significance (Jan 23, 2024)
15-75338653-A-C		not specified	Uncertain significance (Oct 12, 2022)
15-75338659-T-C		not specified	Uncertain significance (Mar 05, 2025)
15-75338987-T-C		not specified	Uncertain significance (Nov 07, 2022)
15-75339008-G-A		not specified	Uncertain significance (Feb 13, 2025)
15-75339029-C-G		not specified	Uncertain significance (Mar 20, 2024)
15-75339056-G-A		not specified	Uncertain significance (Jul 16, 2024)
15-75339090-T-C		not specified	Uncertain significance (Mar 28, 2023)
15-75339269-G-A		not specified	Uncertain significance (Nov 10, 2024)
15-75339270-C-T		not specified	Uncertain significance (Nov 10, 2024)
15-75339285-G-A		not specified	Uncertain significance (Mar 29, 2023)
15-75339341-C-G		not specified	Uncertain significance (Mar 15, 2024)
15-75339703-G-T		not specified	Uncertain significance (Aug 22, 2022)
15-75339713-G-A		not specified	Uncertain significance (Mar 19, 2024)
15-75339717-G-A		not specified	Uncertain significance (Nov 15, 2024)
15-75339719-G-A		not specified	Uncertain significance (Feb 07, 2025)
15-75339792-G-A		not specified	Uncertain significance (Jun 30, 2022)
15-75339806-G-A		not specified	Uncertain significance (Dec 07, 2022)
15-75339812-C-T		not specified	Uncertain significance (Jul 22, 2024)
15-75339843-C-G		not specified	Uncertain significance (Dec 19, 2022)
15-75339976-G-A		not specified	Uncertain significance (Feb 19, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COMMD4	protein_coding	protein_coding	ENST00000267935	8	6037

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000320	0.826	125719	0	27	125746	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0709	118	116	1.02	0.00000679	1264
Missense in Polyphen		32	39.16	0.81715		464
Synonymous	0.220	51	53.0	0.962	0.00000325	408
Loss of Function	1.21	7	11.4	0.613	4.82e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000181	0.000163
Finnish	0.000311	0.000277
European (Non-Finnish)	0.0000824	0.0000791
Middle Eastern	0.000181	0.000163
South Asian	0.0000654	0.0000653
Other	0.000327	0.000326

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. {ECO:0000269|PubMed:15799966, ECO:0000305|PubMed:21778237}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.546
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.332
• ghis: 0.601

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Commd4

Gene ontology

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