FNIP1 p.Pro892=
c.2676C>T · VCV4724278
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, 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 3 | GERP 0.82, phastCons 1 |
| Overall | ||
| CADD | 5.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,179,994 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,030 alleles · very rare
exomes 2/1,461,800 · genomes 0/152,230 · joint denominator
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.Pro892=
- Coding
- c.2676C>T
- MANE Select
- NM_133372
- Type
- single nucleotide variant
- Location
- chr5:131671768 (GRCh38)
- Gene constraint
- LOEUF 0.394 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 55.41 · 1 PDB
- Residue 892
- the cdenn fnip1/2-type domain; a UniProt-annotated variant site (in imd93; undetectable protein in homozygous patient cells)
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-pro892 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown