PER3 p.Gln405=
c.1215A>G · VCV3887833
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0179%, 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 2.3 | GERP -0.47, phastCons 1 |
| Overall | ||
| CADD | 7.293 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0179%
South Asian · 16/89,206 alleles
Filtering AF
0.0112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00916%
Overall
0.00134%
21/1,572,446 alleles · ultra-rare
exomes 21/1,420,088 · genomes 0/152,358 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0179% | 5,575 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 61,060 |
| European (non-Finnish) | 0.00035% | 286,045 |
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.Gln405=
- Coding
- c.1215A>G
- MANE Select
- NM_001377275
- Type
- single nucleotide variant
- Location
- chr1:7808971 (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-gln405 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown