PEPD p.Ala2=
c.6G>A · rs752794552 · VCV1674258
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.044%, 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 0.49 | GERP -2.1, phastCons 0.97 |
| Overall | ||
| CADD | 15.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.044%
East Asian · 19/43,192 alleles
Filtering AF
0.0288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0239%
Overall
0.00184%
29/1,577,560 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.044% | 2,273 |
| Remaining individualsnot grpmax-eligible | 0.00654% | 15,289 |
| South Asian | 0.00577% | 17,335 |
| African / African-American | 0.00134% | 74,428 |
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
- PEPD
- Protein
- p.Ala2=
- Coding
- c.6G>A
- MANE Select
- NM_000285
- dbSNP
- rs752794552
- Type
- single nucleotide variant
- Location
- chr19:33521755 (GRCh38)
- Gene constraint
- LOEUF 1.132 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 97.62 · 21 PDB
- Residue 2
- a modified residue (n-acetylalanine)
Similar variants
- PEPD p.Ala2Val Uncertain significance ★ same residue
- PEPD c.442-1G>C Pathogenic/Likely pathogenic ★★ same type
- PEPD c.504-1G>A Pathogenic/Likely pathogenic ★★ same type
- PEPD c.549-1G>A Pathogenic ★★ same type
- PEPD c.818+2T>G Likely pathogenic ★★ same type
- PEPD c.819-1G>A Likely pathogenic ★★ same type
- PEPD p.Ala212Pro Pathogenic/Likely pathogenic ★★ same type
- PEPD p.Arg184Ter 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/pepd-p-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown