COMMD2

COMM domain containing 2, the group of COMM domain containing

Basic information

Region (hg38): 3:149738472-149752495

Links

ENSG00000114744 ∙ NCBI:51122 ∙ OMIM:616699 ∙ HGNC:24993 ∙ Uniprot:Q86X83 ∙ 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 COMMD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COMMD2 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in COMMD2

This is a list of pathogenic ClinVar variants found in the COMMD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-149741534-C-T		not specified	Uncertain significance (Feb 21, 2024)
3-149741633-T-C		not specified	Likely benign (Jul 19, 2023)
3-149741678-A-C		not specified	Uncertain significance (Jun 06, 2023)
3-149741704-A-T		not specified	Uncertain significance (Apr 12, 2023)
3-149750691-C-T		not specified	Uncertain significance (Oct 27, 2022)
3-149750712-C-G		not specified	Uncertain significance (Nov 09, 2021)
3-149750727-G-A		not specified	Uncertain significance (Oct 03, 2022)
3-149750745-G-A		not specified	Uncertain significance (Mar 22, 2023)
3-149751417-T-C		not specified	Uncertain significance (Dec 06, 2021)
3-149751431-T-C		not specified	Uncertain significance (Apr 13, 2023)
3-149751447-C-T		not specified	Uncertain significance (Dec 30, 2023)
3-149751468-T-C		not specified	Uncertain significance (Apr 22, 2022)
3-149752236-T-G		not specified	Uncertain significance (Feb 15, 2023)
3-149752269-C-A		not specified	Uncertain significance (Nov 18, 2022)
3-149752285-C-T		not specified	Uncertain significance (Jan 19, 2024)
3-149752422-T-G		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COMMD2	protein_coding	protein_coding	ENST00000473414	5	14030

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.54e-9	0.0436	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.689	83	103	0.809	0.00000480	1299
Missense in Polyphen		25	32.939	0.75898		433
Synonymous	-1.13	51	41.7	1.22	0.00000202	383
Loss of Function	-0.611	12	9.92	1.21	5.00e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000334	0.000326
Finnish	0.0000941	0.0000924
European (Non-Finnish)	0.000172	0.000167
Middle Eastern	0.000334	0.000326
South Asian	0.0000733	0.0000653
Other	0.000174	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: 0.108

Intolerance Scores

• loftool: 0.709
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.466
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.288

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Commd2

Gene ontology

• Cellular component: cytoplasm
• Molecular function: protein binding