CSMD1 p.Pro1943=
c.5829C>T · rs145598896 · VCV2658333
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.255%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.229 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.2 |
| Overall | ||
| CADD | 0.061 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.255%
African / African-American · 191/74,864 alleles
Filtering AF
0.225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.214%
Overall
0.116%
1,863/1,605,154 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.255% | 392 |
| European (non-Finnish) | 0.127% | 786 |
| Remaining individualsnot grpmax-eligible | 0.109% | 915 |
| Admixed American | 0.0793% | 1,261 |
| East Asian | 0.0784% | 1,275 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0578% | 1,730 |
| Finnishnot grpmax-eligible | 0.00786% | 12,724 |
| South Asian | 0.00449% | 22,261 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CSMD1
- Protein
- p.Pro1943=
- Coding
- c.5829C>T
- MANE Select
- NM_033225
- dbSNP
- rs145598896
- Type
- single nucleotide variant
- Location
- chr8:3162174 (GRCh38)
- Gene constraint
- LOEUF 0.586 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Residue 1943
- a disulfide bond; the sushi 11 domain
Similar variants
- CSMD1 p.Pro1943Ser Uncertain significance ★ ⚠ same residue
- CSMD1 p.Ala1296Val Uncertain significance ★★ ⚠ same type
- CSMD1 p.Asp908Ala Uncertain significance ★★ ⚠ same type
- CSMD1 p.Asp927Asn Uncertain significance ★★ ⚠ same type
- CSMD1 p.Gln308Leu Uncertain significance ★★ ⚠ same type
- CSMD1 p.Glu1276Asp Uncertain significance ★★ ⚠ same type
- CSMD1 p.Gly3156Arg Uncertain significance ★★ ⚠ same type
- CSMD1 p.Ile1833Thr Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/csmd1-p-pro1943 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown