FASTKD2 p.Pro7=
c.21A>C · rs1478893824 · VCV3054108
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
FASTKD2-related disorder
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 0.069 | GERP -1 |
| Overall | ||
| CADD | 1.125 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,928 alleles
Overall
6.2e-05%
1/1,614,012 alleles · very rare
exomes 0/1,461,814 · genomes 1/152,198 · 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.Pro7=
- Coding
- c.21A>C
- MANE Select
- NM_001136193
- dbSNP
- rs1478893824
- Type
- single nucleotide variant
- Location
- chr2:206766714 (GRCh38)
- Gene constraint
- LOEUF 1.203 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.39
Disease context
FASTKD2-related disorder
Similar variants
- FASTKD2 p.Arg358Ter Pathogenic/Likely pathogenic ★★ same condition
- FASTKD2 p.Leu457= Likely benign same condition
- FASTKD2 p.Val251= Likely benign same condition
- FASTKD2 c.777+7dup Likely benign same condition
- 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.Arg432Ter 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-pro7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown