CSRP3 p.His87=
c.261T>C · rs773476497 · VCV543043
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Conditions
3
hypertrophic cardiomyopathy 12
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 1.7 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 4.598 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,880 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000474%
Overall
0.00103%
15/1,461,870 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,440 |
| European (non-Finnish) | 0.0011% | 90,771 |
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.His87=
- Coding
- c.261T>C
- MANE Select
- NM_003476
- dbSNP
- rs773476497
- Type
- single nucleotide variant
- Location
- chr11:19188156 (GRCh38)
- Gene constraint
- LOEUF 1.307 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.91 · 2 PDB
Similar variants
- CSRP3 p.His87Tyr Uncertain significance ★★ ⚠ same residue
- 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
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-his87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown