FDPS p.Phe83=
c.249C>T · rs765803031 · VCV753832
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -0.13 | GERP -2.5, phastCons 0.015 |
| Overall | ||
| CADD | 9.137 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,074 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00155%
25/1,613,878 alleles · ultra-rare
exomes 22/1,461,718 · genomes 3/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,074 |
| Admixed American | 0.015% | 6,666 |
| African / African-American | 0.00267% | 37,447 |
| East Asian | 0.00223% | 44,894 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,468 |
| South Asian | 0.0011% | 91,084 |
| European (non-Finnish) | 0.000848% | 117,993 |
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
- FDPS
- Protein
- p.Phe83=
- Coding
- c.249C>T
- MANE Select
- NM_002004
- dbSNP
- rs765803031
- Type
- single nucleotide variant
- Location
- chr1:155310115 (GRCh38)
- Gene constraint
- LOEUF 0.744 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.27 · 92 PDB
- Residue 83
- an α-helix
Similar variants
- FDPS c.684+2T>G Likely pathogenic ★ same type
- FDPS p.Ala119Val Uncertain significance ★ ⚠ same type
- FDPS p.Arg110Gly Uncertain significance ★ ⚠ same type
- FDPS p.Arg110Trp Uncertain significance ★ ⚠ same type
- FDPS p.Arg214Gln Uncertain significance ★ ⚠ same type
- FDPS p.Arg23Gln Uncertain significance ★ ⚠ same type
- FDPS p.Arg23Trp Uncertain significance ★ ⚠ same type
- FDPS p.Arg25Lys 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/fdps-p-phe83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown