FASTKD2 p.Phe64=
c.192T>C · rs150457139 · VCV380292
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.483%, eas)
Conditions
1
combined oxidative phosphorylation deficiency 44
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 -0.53 | GERP -3.5 |
| Overall | ||
| CADD | 1.115 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.483%
East Asian · 216/44,676 alleles
Filtering AF
0.431%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.41%
Overall
0.0201%
322/1,599,984 alleles · rare
exomes 263/1,447,634 · genomes 59/152,350 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.483% | 207 |
| Remaining individualsnot grpmax-eligible | 0.089% | 1,124 |
| South Asian | 0.036% | 2,776 |
| African / African-American | 0.0148% | 6,749 |
| Admixed American | 0.00694% | 14,407 |
| European (non-Finnish) | 0.000341% | 293,259 |
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
- FASTKD2
- Protein
- p.Phe64=
- Coding
- c.192T>C
- MANE Select
- NM_001136193
- dbSNP
- rs150457139
- Type
- single nucleotide variant
- Location
- chr2:206766885 (GRCh38)
- Gene constraint
- LOEUF 1.203 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.39
Similar variants
- FASTKD2 c.882-1G>A Pathogenic/Likely pathogenic ★★ same condition
- FASTKD2 c.991-2A>G Likely pathogenic ★★ same condition
- FASTKD2 p.Arg290Ter Pathogenic ★★ same condition
- FASTKD2 p.Arg358Ter Pathogenic/Likely pathogenic ★★ same condition
- FASTKD2 p.Arg432Ter Pathogenic/Likely pathogenic ★★ same condition
- FASTKD2 p.Cys283Ter Pathogenic/Likely pathogenic ★★ same condition
- FASTKD2 p.Gln564Ter Pathogenic/Likely pathogenic ★★ same condition
- FASTKD2 p.Trp302Ter Pathogenic/Likely pathogenic ★★ same condition
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/fastkd2-p-phe64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown