FNIP1 p.Ser232=
c.696T>G · rs542375781 · VCV2804316
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, 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 |
|---|---|---|
| Pangolin | Δ0.20 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/75,010 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000494%
Overall
0.00197%
3/152,326 alleles · very rare
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
- FNIP1
- Protein
- p.Ser232=
- Coding
- c.696T>G
- MANE Select
- NM_133372
- dbSNP
- rs542375781
- Type
- single nucleotide variant
- Location
- chr5:131710588 (GRCh38)
- Gene constraint
- LOEUF 0.394 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 55.41 · 1 PDB
- Residue 232
- the udenn fnip1/2-type domain; a modified residue (phosphoserine; by ampk)
Similar variants
- FNIP1 p.Arg1024Cys Uncertain significance ★★ ⚠ same type
- FNIP1 p.Arg1067Gln Uncertain significance ★★ ⚠ same type
- FNIP1 p.Arg217Gln Uncertain significance ★★ ⚠ same type
- FNIP1 p.Arg226His Uncertain significance ★★ ⚠ same type
- FNIP1 p.Arg326Gln Uncertain significance ★★ same type
- FNIP1 p.Arg518Trp Uncertain significance ★★ ⚠ same type
- FNIP1 p.Arg667Thr Uncertain significance ★★ ⚠ same type
- FNIP1 p.Asn186Ser 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/fnip1-p-ser232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown