CSRP3 p.Lys32=
c.96G>A · rs1565053085 · VCV585276
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Conditions
1
dilated cardiomyopathy
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 5.9 | GERP 5.8, phastCons 1 |
| Overall | ||
| CADD | 12.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,076 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000137%
2/1,461,736 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.Lys32=
- Coding
- c.96G>A
- MANE Select
- NM_003476
- dbSNP
- rs1565053085
- Type
- single nucleotide variant
- Location
- chr11:19192353 (GRCh38)
- Gene constraint
- LOEUF 1.307 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.91 · 2 PDB
- Residue 32
- the lim zinc-binding 1 domain; a turn
Similar variants
- CSRP3 p.Lys32Arg Uncertain significance ★★ ⚠ same residue
- CSRP3 p.Gly78Val Uncertain significance ★★ ⚠ same condition
- CSRP3 p.Ala112= Benign ★★ same condition
- CSRP3 p.Trp4Arg Conflicting classifications of pathogenicity ★ ⚠ same condition
- CSRP3 p.Glu118= Likely pathogenic same condition
- CSRP3 p.Thr16Ser Likely pathogenic ⚠ same condition
- CSRP3 p.Trp140Cys Pathogenic same condition
- CSRP3 c.414+1G>T Likely pathogenic ★★ 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/csrp3-p-lys32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown