FRMPD4 p.Pro85=
c.255C>T · rs769101701 · VCV745909
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00529%, sas)
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 -4.7 | GERP -4.2 |
| Overall | ||
| CADD | 0.991 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00529%
South Asian · 3/56,710 alleles
Filtering AF
0.0014%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000689%
Overall
0.000579%
7/1,209,019 alleles · very rare
exomes 6/1,097,444 · genomes 1/111,575 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00529% | 18,903 |
| East Asian | 0.00296% | 33,754 |
| African / African-American | 0.00175% | 57,016 |
| European (non-Finnish) | 0.000224% | 447,255 |
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
- FRMPD4
- Protein
- p.Pro85=
- Coding
- c.255C>T
- MANE Select
- NM_001368397
- dbSNP
- rs769101701
- Type
- single nucleotide variant
- Location
- chrX:12609817 (GRCh38)
- Structure
- AlphaFold pLDDT 54.86 · 5 PDB
- Residue 85
- the pdz domain
Similar variants
- FRMPD4 p.Ala1297Pro Uncertain significance ★★ ⚠ same type
- FRMPD4 p.Ala728Pro Uncertain significance ★★ ⚠ same type
- FRMPD4 p.Ala728Val Uncertain significance ★★ ⚠ same type
- FRMPD4 p.Ala809Thr Uncertain significance ★★ ⚠ same type
- FRMPD4 p.Arg1288Gln Uncertain significance ★★ ⚠ same type
- FRMPD4 p.Arg422Cys Uncertain significance ★★ ⚠ same type
- FRMPD4 p.Asn1270Ile Uncertain significance ★★ ⚠ same type
- FRMPD4 p.Asn545Lys 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/frmpd4-p-pro85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown