CSRP3 p.Arg41=
c.123G>A · rs1590104476 · VCV760586
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
3
Cardiovascular phenotype
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 0.41 | GERP 3.9, phastCons 0.99 |
| Overall | ||
| CADD | 8.499 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,028 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,460,078 alleles · very rare
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
- CSRP3
- Protein
- p.Arg41=
- Coding
- c.123G>A
- MANE Select
- NM_003476
- dbSNP
- rs1590104476
- Type
- single nucleotide variant
- Location
- chr11:19188294 (GRCh38)
- Gene constraint
- LOEUF 1.307 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.91 · 2 PDB
- Residue 41
- the lim zinc-binding 1 domain
Similar variants
- CSRP3 c.414+1G>T Likely pathogenic ★★ same condition
- CSRP3 p.Cys37Ter Pathogenic/Likely pathogenic ★★ same condition
- CSRP3 p.Cys58Gly Pathogenic ★★ same condition
- CSRP3 p.Lys113Ter Pathogenic ★★ same condition
- CSRP3 c.113-3C>T Uncertain significance ★★ same condition
- CSRP3 c.414+6A>G Uncertain significance ★★ same condition
- CSRP3 c.415-1G>A Uncertain significance ★★ same condition
- CSRP3 c.*159C>T Uncertain significance ★★ same condition
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/csrp3-p-arg41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown