CSMD2

protein-coding

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

Gene summary

The protein encoded by this gene is thought to be involved in the control of complement cascade of the immune system. Defects in this gene have been associated with schizophrenia. This gene may act as a tumor suppressor for colorectal cancer. [provided by RefSeq, Jan 2020]

MANE transcript

NM_001281956.2

Inheritance

—

ClinVar variants

U:472B:29

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

Max pathogenic AF

—

Genomic locus

chr1:33,513,998-34,165,842

External References & Databases

Ensembl (ENSG00000121904)

Transcript & Mutation Effects

hg38 • Region Span ~651.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CSMD2 variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 499

not providedTotal: 23

EBV-positive nodal T- and NK-cell lymphomaTotal: 2

AutismTotal: 1

Prostate cancerTotal: 1

Autism spectrum disorderTotal: 1

Attention deficit hyperactivity disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001281956.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	16 clinvar	1 clinvar	19
missense			462 clinvar	12 clinvar		474
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	472	28	1	501

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001281956.2	RefSeq	NP_001268885.1	70	MANE Select
ENST00000373381.9	Ensembl	ENSP00000362479.4	70	MANE Select
NM_052896.5	RefSeq	NP_443128.2	69	Standard
ENST00000373388.7	Ensembl	ENSP00000362486.3	69	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

plasma membrane
integral component of membrane

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.316
RVIS EVS: -1.92
RVIS percentile EVS: 1.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.176

Gene Damage Prediction

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