PER3 p.Ala163=
c.489G>A · rs191955069 · VCV3038806
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.105%, afr)
Conditions
1
PER3-related disorder
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 0.24 | GERP -3.4, phastCons 0.003 |
| Overall | ||
| CADD | 6.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.105%
African / African-American · 79/75,026 alleles
Filtering AF
0.0866%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0797%
Overall
0.00675%
109/1,613,846 alleles · rare
exomes 69/1,461,568 · genomes 40/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.105% | 950 |
| Middle Eastern | 0.0495% | 2,020 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,208 |
| Admixed American | 0.00333% | 30,008 |
| European (non-Finnish) | 0.0011% | 90,751 |
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
- PER3
- Protein
- p.Ala163=
- Coding
- c.489G>A
- MANE Select
- NM_001377275
- dbSNP
- rs191955069
- Type
- single nucleotide variant
- Location
- chr1:7788143 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.62
- Residue 163
- the pas 1 domain
Disease context
PER3-related disorder
Similar variants
- PER3 p.Ala163Val Uncertain significance ★ ⚠ same residue
- PER3 c.275-9G>A Likely benign same condition
- PER3 p.Ala18Ser Likely benign same condition
- PER3 p.Gly1196= Likely benign same condition
- PER3 p.Met1037Thr Likely benign same condition
- PER3 p.Thr1019= Benign same condition
- PER3 p.Thr306= Likely benign same condition
- PER3 p.Thr626= Likely benign same condition
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/per3-p-ala163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown