FARSA p.Asp260=
c.780C>T · rs143258144 · VCV2649358
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0274%, sas)
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 -3.8 | GERP -3.4 |
| Overall | ||
| CADD | 2.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0274%
South Asian · 25/91,086 alleles
Filtering AF
0.019%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0163%
Overall
0.00235%
38/1,614,020 alleles · ultra-rare
exomes 35/1,461,882 · genomes 3/152,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0274% | 3,643 |
| Middle Eastern | 0.0164% | 6,084 |
| Admixed American | 0.005% | 19,996 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| African / African-American | 0.00133% | 74,914 |
| European (non-Finnish) | 0.000508% | 196,672 |
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
- FARSA
- Protein
- p.Asp260=
- Coding
- c.780C>T
- MANE Select
- NM_004461
- dbSNP
- rs143258144
- Type
- single nucleotide variant
- Location
- chr19:12928403 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.43 · 3 PDB
- Residue 260
- an α-helix
Similar variants
- FARSA p.Pro347Leu Likely pathogenic ★★ same type
- FARSA p.Arg338Cys Uncertain significance ★★ ⚠ same type
- FARSA p.Gly306Ser Uncertain significance ★★ ⚠ same type
- FARSA c.1027-17T>C Benign ★★ same type
- FARSA p.Arg271His Pathogenic ★ same type
- FARSA p.Phe256Leu Pathogenic ★ same type
- FARSA p.Ala148Thr Uncertain significance ★ ⚠ same type
- FARSA p.Ala283Val 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/farsa-p-asp260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown