CSMD2

CUB and Sushi multiple domains 2, the group of Complement system regulators and receptors|Sushi domain containing

Basic information

Region (hg38): 1:33513997-34165842

Links

ENSG00000121904 ∙ NCBI:114784 ∙ OMIM:608398 ∙ HGNC:19290 ∙ Uniprot:Q7Z408 ∙ 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 CSMD2 gene.

• Inborn genetic diseases (136 variants)
• not provided (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSMD2 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				16	1	17
missense			128	5		133
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	133	21	1

Variants in CSMD2

This is a list of pathogenic ClinVar variants found in the CSMD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-33519551-C-G		not specified	Uncertain significance (Dec 16, 2022)
1-33519561-C-G		not specified	Likely benign (Apr 19, 2023)
1-33519595-C-T		not specified	Uncertain significance (Jun 28, 2023)
1-33519618-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-33519663-A-T		not specified	Uncertain significance (Apr 26, 2023)
1-33519675-C-G		not specified	Uncertain significance (Aug 18, 2021)
1-33519900-A-C		not specified	Uncertain significance (Sep 16, 2021)
1-33521478-C-T		not specified	Uncertain significance (Jul 27, 2021)
1-33521480-A-G		not specified	Uncertain significance (Oct 26, 2021)
1-33521486-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-33523360-C-T		not specified	Uncertain significance (Jan 04, 2022)
1-33524945-C-A		not specified	Uncertain significance (Jan 02, 2024)
1-33524978-G-T		not specified	Uncertain significance (Jun 29, 2023)
1-33524986-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-33525038-C-A		not specified	Uncertain significance (Mar 01, 2024)
1-33527219-T-G		not specified	Uncertain significance (Mar 20, 2023)
1-33527223-G-A		not specified	Uncertain significance (May 05, 2023)
1-33527252-C-T			Likely benign (May 01, 2023)
1-33533198-C-T			Likely benign (May 01, 2022)
1-33533199-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-33533205-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-33533813-G-T		not specified	Uncertain significance (Jul 20, 2021)
1-33537031-C-G		not specified	Uncertain significance (Nov 03, 2023)
1-33537531-G-A		not specified	Uncertain significance (Oct 20, 2023)
1-33537547-A-G		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.316
• rvis_EVS: -1.92
• rvis_percentile_EVS: 1.92

Haploinsufficiency Scores

• pHI: 0.568
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.176

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csmd2

Gene ontology

• Cellular component: plasma membrane;integral component of membrane