F2RL1 p.Ser363=
c.1089T>C · rs138965893 · VCV718860
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.216%, nfe)
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 -7.6 | GERP -5 |
| Overall | ||
| CADD | 0.549 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.216%
European (non-Finnish) · 2,553/1,180,002 alleles
Filtering AF
0.209%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.206%
Overall
0.176%
2,842/1,614,038 alleles · rare
exomes 2,644/1,461,882 · genomes 198/152,156 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.216% | 462 |
| Finnishnot grpmax-eligible | 0.177% | 566 |
| Remaining individualsnot grpmax-eligible | 0.176% | 568 |
| Admixed American | 0.0433% | 2,308 |
| African / African-American | 0.04% | 2,501 |
| Middle Eastern | 0.0165% | 6,062 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,867 |
| South Asian | 0.00659% | 15,180 |
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
- F2RL1
- Protein
- p.Ser363=
- Coding
- c.1089T>C
- MANE Select
- NM_005242
- dbSNP
- rs138965893
- Type
- single nucleotide variant
- Location
- chr5:76833696 (GRCh38)
- Gene constraint
- LOEUF 0.989 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.92 · 7 PDB
Similar variants
- F2RL1 p.Arg2= Benign ★★ same type
- F2RL1 p.Ala12Val Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala188Thr Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala18Ser Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala220Val Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala273Thr Uncertain significance ★ ⚠ same type
- F2RL1 p.Ala358Thr Uncertain significance ★ ⚠ same type
- F2RL1 p.Arg284Lys Uncertain significance ★ ⚠ 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/f2rl1-p-ser363 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown