CATSPER2 p.Thr384=
c.1152G>A · VCV4280825
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.19 | GERP -3.4 |
| Overall | ||
| CADD | 5.628 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.267%
African / African-American · 198/74,240 alleles
Filtering AF
0.236%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.225%
Overall
0.114%
1,830/1,609,042 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.267% | 375 |
| European (non-Finnish) | 0.13% | 770 |
| Remaining individualsnot grpmax-eligible | 0.0929% | 1,077 |
| Finnishnot grpmax-eligible | 0.0359% | 2,786 |
| Admixed American | 0.0251% | 3,985 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,580 |
| South Asian | 0.0033% | 30,332 |
| East Asian | 0.00223% | 44,814 |
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.Thr384=
- Coding
- c.1152G>A
- MANE Select
- NM_172095
- Type
- single nucleotide variant
- Location
- chr15:43635386 (GRCh38)
- Gene constraint
- LOEUF 1.047 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 69.83
- Residue 384
- the 'disordered' region
Similar variants
- CATSPER2 p.Thr384Met Likely benign ★ same residue
- 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
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-thr384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown