CATSPERD p.Ser414=
c.1242G>A · VCV3263554
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0513%, 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 -1.7 | GERP -4.3 |
| Overall | ||
| CADD | 0.399 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0513%
East Asian · 23/44,874 alleles
Filtering AF
0.035%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0296%
Overall
0.00446%
72/1,613,706 alleles · ultra-rare
exomes 68/1,461,650 · genomes 4/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0513% | 1,951 |
| African / African-American | 0.024% | 4,165 |
| Middle Eastern | 0.0165% | 6,054 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| South Asian | 0.00659% | 15,178 |
| Finnishnot grpmax-eligible | 0.00156% | 64,000 |
| European (non-Finnish) | 0.00153% | 65,544 |
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
- CATSPERD
- Protein
- p.Ser414=
- Coding
- c.1242G>A
- MANE Select
- NM_152784
- Type
- single nucleotide variant
- Location
- chr19:5754209 (GRCh38)
- Gene constraint
- LOEUF 0.998 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.43
Similar variants
- CATSPERD p.Ser414Leu Likely benign ★ same residue
- CATSPERD p.Ala101Val Uncertain significance ★ ⚠ same type
- CATSPERD p.Ala248Thr Uncertain significance ★ ⚠ same type
- CATSPERD p.Ala307Glu Uncertain significance ★ ⚠ same type
- CATSPERD p.Ala307Thr Uncertain significance ★ ⚠ same type
- CATSPERD p.Ala331Ser Uncertain significance ★ ⚠ same type
- CATSPERD p.Ala375Val Uncertain significance ★ ⚠ same type
- CATSPERD p.Ala524Thr Uncertain significance ★ ⚠ 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/catsperd-p-ser414 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown