PER3 p.Ile479=
c.1437T>C · rs143456316 · VCV2638143
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.124%, 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 -4.4 | GERP -4.9 |
| Overall | ||
| CADD | 0.333 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.124%
African / African-American · 93/75,014 alleles
Filtering AF
0.104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.096%
Overall
0.00601%
97/1,613,490 alleles · rare
exomes 45/1,461,242 · genomes 52/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.124% | 807 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,828 |
| Admixed American | 0.00167% | 59,944 |
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.Ile479=
- Coding
- c.1437T>C
- MANE Select
- NM_001377275
- dbSNP
- rs143456316
- Type
- single nucleotide variant
- Location
- chr1:7810503 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.62
Similar variants
- PER3 p.Arg157His Uncertain significance ★★ ⚠ same type
- PER3 p.Asn572Thr Uncertain significance ★★ ⚠ same type
- PER3 p.Ala980= Benign ★★ same type
- PER3 p.Cys1185Ser Benign ★★ same type
- PER3 p.Ile614= Benign ★★ same type
- PER3 p.Leu937= Likely benign ★★ same type
- PER3 p.Thr527Ala Likely benign ★★ same type
- PER3 p.Thr983= Benign/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/per3-p-ile479 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown