CSMD1 p.Ser541=
c.1623C>T · rs375577340 · VCV714372
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.07%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP -0.71, phastCons 0.12 |
| Overall | ||
| CADD | 8.655 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.07%
African / African-American · 805/74,986 alleles
Filtering AF
1.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.987%
Overall
0.0636%
1,024/1,611,092 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.07% | 93 |
| Admixed American | 0.0821% | 1,219 |
| Remaining individualsnot grpmax-eligible | 0.0705% | 1,418 |
| Middle Eastern | 0.0497% | 2,014 |
| European (non-Finnish) | 0.0104% | 9,661 |
| Finnishnot grpmax-eligible | 0.00157% | 63,852 |
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.Ser541=
- Coding
- c.1623C>T
- MANE Select
- NM_033225
- dbSNP
- rs375577340
- Type
- single nucleotide variant
- Location
- chr8:3409544 (GRCh38)
- Gene constraint
- LOEUF 0.586 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Residue 541
- the sushi 3 domain; a disulfide bond
Similar variants
- 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
- CSMD1 p.Lys1718Asn 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-ser541 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown