FASTKD2 p.Pro570=
c.1710A>G · rs537680468 · VCV1608178
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 -2.7 | GERP 0.23 |
| Overall | ||
| CADD | 0.098 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,010 alleles
Filtering AF
0.000359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000744%
12/1,613,722 alleles · very rare
exomes 11/1,461,412 · genomes 1/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,010 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
| South Asian | 0.0011% | 91,072 |
| European (non-Finnish) | 0.000763% | 131,074 |
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.Pro570=
- Coding
- c.1710A>G
- MANE Select
- NM_001136193
- dbSNP
- rs537680468
- Type
- single nucleotide variant
- Location
- chr2:206788052 (GRCh38)
- Gene constraint
- LOEUF 1.203 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.39
- Residue 570
- a UniProt-annotated variant site (in coxpd44; decreased mitochondrial large ribosomal subunit assembly); a UniProt-annotated variant site (in coxpd44)
Similar variants
- FASTKD2 c.882-1G>A Pathogenic/Likely pathogenic ★★ same type
- FASTKD2 c.991-2A>G Likely pathogenic ★★ same type
- FASTKD2 p.Arg290Ter Pathogenic ★★ same type
- FASTKD2 p.Arg358Ter Pathogenic/Likely pathogenic ★★ same type
- FASTKD2 p.Arg432Ter Pathogenic/Likely pathogenic ★★ same type
- FASTKD2 p.Cys283Ter Pathogenic/Likely pathogenic ★★ same type
- FASTKD2 p.Gln564Ter Pathogenic/Likely pathogenic ★★ same type
- FASTKD2 p.Trp302Ter Pathogenic/Likely pathogenic ★★ 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/fastkd2-p-pro570 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown