CSMD2 p.Phe834=
c.2502C>T · rs143617019 · VCV2638635
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.568%, 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 -6 | GERP -5.5 |
| Overall | ||
| CADD | 3.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.568%
African / African-American · 426/74,974 alleles
Filtering AF
0.524%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.506%
Overall
0.0304%
490/1,609,954 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.568% | 176 |
| Middle Eastern | 0.0496% | 2,015 |
| Remaining individualsnot grpmax-eligible | 0.0385% | 2,595 |
| Admixed American | 0.0318% | 3,146 |
| East Asian | 0.00447% | 22,368 |
| European (non-Finnish) | 0.00127% | 78,492 |
| South Asian | 0.00111% | 90,428 |
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
- CSMD2
- Protein
- p.Phe834=
- Coding
- c.2502C>T
- MANE Select
- NM_001281956
- dbSNP
- rs143617019
- Type
- single nucleotide variant
- Location
- chr1:33726552 (GRCh38)
- Gene constraint
- LOEUF 0.364 · pLI 1.00 (gnomAD)
- Residue 834
- the cub 5 domain
Similar variants
- CSMD2 p.Pro1506= Likely benign ★★ same type
- CSMD2 p.Ser3015= Benign ★★ same type
- CSMD2 c.404+2T>A Uncertain significance ★ same type
- CSMD2 c.6344-398G>T Uncertain significance ★ same type
- CSMD2 c.6344-422A>G Uncertain significance ★ same type
- CSMD2 c.6344-423T>C Uncertain significance ★ same type
- CSMD2 c.6344-429G>A Uncertain significance ★ same type
- CSMD2 c.6344-435G>A 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/csmd2-p-phe834 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown