CATSPER2 p.Ser447=
c.1341C>A · rs140242525 · VCV2645275
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.383%, eas)
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 -2 | GERP -1.5 |
| Overall | ||
| CADD | 0.343 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.383%
East Asian · 171/44,682 alleles
Filtering AF
0.336%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.318%
Overall
0.0522%
840/1,608,196 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.383% | 261 |
| Remaining individualsnot grpmax-eligible | 0.0482% | 2,074 |
| European (non-Finnish) | 0.0473% | 2,115 |
| African / African-American | 0.0348% | 2,877 |
| South Asian | 0.033% | 3,026 |
| Admixed American | 0.0218% | 4,592 |
| Finnishnot grpmax-eligible | 0.0188% | 5,310 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00681% | 14,693 |
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
- CATSPER2
- Protein
- p.Ser447=
- Coding
- c.1341C>A
- MANE Select
- NM_172095
- dbSNP
- rs140242525
- Type
- single nucleotide variant
- Location
- chr15:43632772 (GRCh38)
- Gene constraint
- LOEUF 1.047 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 69.83
- Residue 447
- the 'disordered' region
Similar variants
- CATSPER2 p.Arg498Ter Uncertain significance ★★ same type
- CATSPER2 c.1178+188A>G Benign ★★ same type
- CATSPER2 c.1179-15A>C Benign ★★ same type
- CATSPER2 c.1179-2A>T Benign ★★ same type
- CATSPER2 c.1179-3A>C Benign ★★ same type
- CATSPER2 c.1179-8T>C Benign ★★ same type
- CATSPER2 c.1397-121C>T Benign ★★ same type
- CATSPER2 c.1397-29G>A 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/catsper2-p-ser447 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown