PTF1A p.Leu289=
c.867C>G · rs549237556 · VCV732610
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.09%, 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 1.1 | GERP 0.84, phastCons 1 |
| Overall | ||
| CADD | 9.892 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.09%
South Asian · 82/91,070 alleles
Filtering AF
0.0743%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0685%
Overall
0.00527%
85/1,613,788 alleles · ultra-rare
exomes 79/1,461,534 · genomes 6/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.09% | 1,111 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
| European (non-Finnish) | 8.48e-05% | 1,179,768 |
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
- PTF1A
- Protein
- p.Leu289=
- Coding
- c.867C>G
- MANE Select
- NM_178161
- dbSNP
- rs549237556
- Type
- single nucleotide variant
- Location
- chr10:23193786 (GRCh38)
- Gene constraint
- LOEUF 1.878 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.81
Similar variants
- PTF1A p.Pro191Thr Pathogenic/Likely pathogenic ★★ same type
- PTF1A p.Ala149Val Uncertain significance ★★ ⚠ same type
- PTF1A p.Ala3Val Uncertain significance ★★ ⚠ same type
- PTF1A p.Arg206Leu Uncertain significance ★★ ⚠ same type
- PTF1A p.Arg63Cys Uncertain significance ★★ ⚠ same type
- PTF1A p.Asp270His Uncertain significance ★★ ⚠ same type
- PTF1A p.Cys121Tyr Uncertain significance ★★ ⚠ same type
- PTF1A p.Gly143Glu 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/ptf1a-p-leu289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown