COMMD5

COMM domain containing 5, the group of COMM domain containing

Basic information

Region (hg38): 8:144841042-144853736

Links

ENSG00000170619 ∙ NCBI:28991 ∙ OMIM:608216 ∙ HGNC:17902 ∙ Uniprot:Q9GZQ3 ∙ 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 COMMD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COMMD5 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in COMMD5

This is a list of pathogenic ClinVar variants found in the COMMD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144841361-C-T		not specified	Uncertain significance (Jun 29, 2023)
8-144841365-T-G		not specified	Uncertain significance (Dec 31, 2023)
8-144841385-C-T		not specified	Uncertain significance (Aug 27, 2024)
8-144841393-G-A		not specified	Uncertain significance (Oct 08, 2024)
8-144841426-A-G		not specified	Uncertain significance (Nov 21, 2024)
8-144841465-C-G		not specified	Uncertain significance (Sep 30, 2021)
8-144841496-T-G		not specified	Uncertain significance (Jul 26, 2024)
8-144841526-G-T		not specified	Uncertain significance (Apr 19, 2023)
8-144841540-G-A		not specified	Uncertain significance (Apr 06, 2024)
8-144841561-T-C		not specified	Uncertain significance (Sep 18, 2024)
8-144841639-G-A		not specified	Uncertain significance (Jul 18, 2024)
8-144841657-C-G		not specified	Uncertain significance (Feb 10, 2022)
8-144841679-C-T		not specified	Uncertain significance (Apr 04, 2024)
8-144841683-A-C		not specified	Uncertain significance (Dec 01, 2022)
8-144841715-A-G		not specified	Likely benign (Nov 18, 2022)
8-144841804-T-C		not specified	Likely benign (Oct 30, 2024)
8-144841945-T-G		not specified	Uncertain significance (Jun 10, 2024)
8-144841973-T-G		not specified	Uncertain significance (Jan 03, 2024)
8-144841988-T-C		not specified	Uncertain significance (Feb 05, 2024)
8-144842024-A-G		not specified	Uncertain significance (Jun 24, 2022)
8-144842105-C-T		not specified	Uncertain significance (Dec 09, 2024)
8-144842116-C-T		not specified	Uncertain significance (Sep 10, 2024)
8-144842147-C-T		not specified	Uncertain significance (Jun 24, 2022)
8-144842273-C-T		not specified	Uncertain significance (Jul 26, 2024)
8-144842295-C-A		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COMMD5	protein_coding	protein_coding	ENST00000450361	1	12695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000150	0.248	125712	0	25	125737	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.465	122	137	0.888	0.00000838	1429
Missense in Polyphen		31	35.384	0.8761		378
Synonymous	0.258	57	59.5	0.957	0.00000334	503
Loss of Function	-0.205	7	6.44	1.09	4.51e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.000115	0.000109
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000115	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate activity of cullin-RING E3 ubiquitin ligase (CRL) complexes (PubMed:21778237). Negatively regulates cell proliferation. Negatively regulates cell cycle G2/M phase transition probably by transactivating p21/CDKN1A through the p53/TP53-independent signaling pathway. Involved in kidney proximal tubule morphogenesis (By similarity). Down-regulates activation of NF-kappa-B (PubMed:15799966). {ECO:0000250|UniProtKB:Q9ERR2, ECO:0000269|PubMed:15799966, ECO:0000305|PubMed:21778237}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.0984

Intolerance Scores

• loftool: 0.875
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.35

Haploinsufficiency Scores

• pHI: 0.0791
• hipred: N
• hipred_score: 0.197
• ghis: 0.495

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.202

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Commd5

Gene ontology

• Cellular component: nucleoplasm;cytosol
• Molecular function: protein binding