CSMD2

Chr 1

CUB and Sushi multiple domains 2

Also known as: dJ1007G16.1, dJ1007G16.2, dJ947L8.1

NCBI Gene: 114784ENSG00000121904UniProt: Q7Z408OMIM: 608398

CSMD2 encodes a protein involved in controlling the complement cascade of the immune system. Mutations in this gene have been associated with schizophrenia, though the inheritance pattern and specific neurological phenotypes in pediatric patients remain to be fully characterized. The gene may also function as a tumor suppressor in colorectal cancer.

OMIMResearchSummary from RefSeq
Multiplemechanism
Clinical Summary— CSMD2
📋
ClinVar Variants
8 unique Pathogenic / Likely Pathogenic· 403 VUS of 479 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

DN
0.6454th %ile
GOF
0.6639th %ile
LOF
0.3939th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

479 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic6
Likely Pathogenic2
VUS403
Likely Benign26
Benign1
6
Pathogenic
2
Likely Pathogenic
403
VUS
26
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
6
0
6
Likely Pathogenic
0
0
2
0
2
VUS
2
394
7
0
403
Likely Benign
0
9
0
17
26
Benign
0
0
0
1
1
Total24031518438

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CSMD2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Variants in CSMD2 and CSMD3, genes involved in synaptogenesis, are associated with epilepsies.
Li X et al.·Epilepsia
2025
A genetic association study of CSMD1 and CSMD2 with cognitive function.
Athanasiu L et al.·Brain Behav Immun
2017
A Genome-Wide Association Study and Rare Variant Analysis for Dupuytren Disease in a North American Population.
Grandizio LC et al.·J Hand Surg Am
2025
Long-read sequencing unveils novel somatic variants and methylation patterns in the genetic information system of early lung cancer.
Cui X et al.·Comput Biol Med
2024
Sequencing of sporadic Attention-Deficit Hyperactivity Disorder (ADHD) identifies novel and potentially pathogenic de novo variants and excludes overlap with genes associated with autism spectrum disorder.
Kim DS et al.·Am J Med Genet B Neuropsychiatr Genet
2017
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients