FASTKD2 p.Ser70=
c.210A>T · rs778865889 · VCV1976146
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000427%, nfe)
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 0.29 | GERP -2.7 |
| Overall | ||
| CADD | 1.747 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000427%
European (non-Finnish) · 5/1,171,980 alleles
Filtering AF
0.000125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.1e-05%
Overall
0.000313%
5/1,598,314 alleles · very rare
exomes 5/1,445,952 · genomes 0/152,362 · 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
- FASTKD2
- Protein
- p.Ser70=
- Coding
- c.210A>T
- MANE Select
- NM_001136193
- dbSNP
- rs778865889
- Type
- single nucleotide variant
- Location
- chr2:206766903 (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 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-ser70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown