CSMD3 p.Tyr116=
c.348C>T · rs35125143 · VCV709345
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.19%, 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 -3 | |
| Overall | ||
| CADD | 1.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.19%
African / African-American · 1,642/74,884 alleles
Filtering AF
2.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.07%
Overall
0.125%
2,008/1,609,844 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.19% | 46 |
| Admixed American | 0.285% | 351 |
| Remaining individualsnot grpmax-eligible | 0.14% | 717 |
| Middle Eastern | 0.0827% | 1,209 |
| East Asian | 0.0246% | 4,067 |
| South Asian | 0.00879% | 11,373 |
| European (non-Finnish) | 0.00714% | 14,005 |
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
- CSMD3
- Protein
- p.Tyr116=
- Coding
- c.348C>T
- MANE Select
- NM_198123
- dbSNP
- rs35125143
- Type
- single nucleotide variant
- Location
- chr8:113314624 (GRCh38)
- Gene constraint
- LOEUF 0.464 · pLI 0.97 (gnomAD)
- Residue 116
- the cub 1 domain
Similar variants
- CSMD3 p.Glu2761Val Uncertain significance ★★ same type
- CSMD3 p.Leu3027Phe Uncertain significance ★★ same type
- CSMD3 c.4896-3C>T Benign ★★ same type
- CSMD3 p.Arg1020His Benign ★★ same type
- CSMD3 p.Arg1228Gln Likely benign ★★ same type
- CSMD3 p.Arg687= Benign/Likely benign ★★ same type
- CSMD3 p.Asp1025= Benign ★★ same type
- CSMD3 p.Asp1473= Benign ★★ 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/csmd3-p-tyr116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown