PEPD p.Arg27=
c.81G>A · rs774960807 · VCV2044069
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
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 -0.009 | GERP 0.68, phastCons 0.72 |
| Overall | ||
| CADD | 12.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,088 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000136%
Overall
0.000248%
4/1,614,002 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,544 |
| European (non-Finnish) | 0.000169% | 590,005 |
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.Arg27=
- Coding
- c.81G>A
- MANE Select
- NM_000285
- dbSNP
- rs774960807
- Type
- single nucleotide variant
- Location
- chr19:33512713 (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 27
- an α-helix
Similar variants
- PEPD p.Arg27Trp Likely pathogenic ★ same residue
- PEPD p.Arg27Gln 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
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-arg27 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown