PER3 p.Ala980=
c.2940A>G · rs116369722 · VCV787732
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.96%, 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 -2.2 | GERP -1.2 |
| Overall | ||
| CADD | 0.998 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.96%
African / African-American · 2,964/74,910 alleles
Filtering AF
3.84%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.79%
Overall
0.239%
3,857/1,613,970 alleles · low-frequency
exomes 2,125/1,461,750 · genomes 1,732/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.96% | 25 |
| Middle Eastern | 1.54% | 65 |
| Remaining individualsnot grpmax-eligible | 0.326% | 306 |
| Admixed American | 0.298% | 335 |
| Ashkenazi Jewishnot grpmax-eligible | 0.138% | 722 |
| South Asian | 0.0417% | 2,397 |
| European (non-Finnish) | 0.0284% | 3,522 |
| East Asian | 0.00669% | 14,952 |
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.Ala980=
- Coding
- c.2940A>G
- MANE Select
- NM_001377275
- dbSNP
- rs116369722
- Type
- single nucleotide variant
- Location
- chr1:7829887 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.62
- Residue 980
- the 'disordered' region; the '5 x 18 aa tandem repeats of s-[hp]-[ap]-t-[at]-[gst]-[atv]-l-s-[mt]-g-[ls]-p-p-[mrs]-[ekr]-[nst]-p' region
Similar variants
- PER3 p.Arg157His Uncertain significance ★★ ⚠ same type
- PER3 p.Asn572Thr Uncertain significance ★★ ⚠ 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
- PER3 p.Tyr65= 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-ala980 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown