PER3 p.Ile614=
c.1842A>T · rs17031601 · VCV780747
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.18%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.52 | GERP -2.9 |
| Overall | ||
| CADD | 0.637 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.18%
African / African-American · 3,138/75,034 alleles
Filtering AF
4.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.01%
Overall
0.227%
3,670/1,614,104 alleles · low-frequency
exomes 1,894/1,461,788 · genomes 1,776/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.18% | 24 |
| Middle Eastern | 0.462% | 216 |
| Remaining individualsnot grpmax-eligible | 0.333% | 301 |
| Admixed American | 0.215% | 465 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,401 |
| European (non-Finnish) | 0.0131% | 7,662 |
| South Asian | 0.00988% | 10,119 |
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.Ile614=
- Coding
- c.1842A>T
- MANE Select
- NM_001377275
- dbSNP
- rs17031601
- Type
- single nucleotide variant
- Location
- chr1:7820525 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.62
- Residue 614
- the 'csnk1e binding domain' region
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.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-ile614 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown