PER2 p.Phe393=
c.1179C>T · rs115692307 · VCV714473
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.81%, afr)
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 -2.6 | GERP -4.2 |
| Overall | ||
| CADD | 4.484 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.81%
African / African-American · 1,360/74,988 alleles
Filtering AF
1.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.7%
Overall
0.161%
2,593/1,613,980 alleles · low-frequency
exomes 1,716/1,461,812 · genomes 877/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.81% | 55 |
| Middle Eastern | 0.396% | 253 |
| Admixed American | 0.233% | 429 |
| Remaining individualsnot grpmax-eligible | 0.194% | 517 |
| European (non-Finnish) | 0.0786% | 1,273 |
| South Asian | 0.0187% | 5,357 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,802 |
| Finnishnot grpmax-eligible | 0.00313% | 31,998 |
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
- PER2
- Protein
- p.Phe393=
- Coding
- c.1179C>T
- MANE Select
- NM_022817
- dbSNP
- rs115692307
- Type
- single nucleotide variant
- Location
- chr2:238262319 (GRCh38)
- Gene constraint
- LOEUF 0.67 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.96 · 4 PDB
Similar variants
- PER2 p.Phe393Leu Uncertain significance ★ ⚠ same residue
- PER2 p.Arg401His Uncertain significance ★★ ⚠ same type
- PER2 p.Glu184Ala Uncertain significance ★★ ⚠ same type
- PER2 p.Ala655= Benign ★★ same type
- PER2 p.Arg401Cys Benign ★★ same type
- PER2 p.Arg820= Likely benign ★★ same type
- PER2 p.Cys1084Arg Likely benign ★★ same type
- PER2 p.His476Asn Likely 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/per2-p-phe393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown