PATL2 p.Pro382=
c.1146C>G · rs190933513 · VCV3049657
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.461%, afr)
Conditions
1
PATL2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.94 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 6.536 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.461%
African / African-American · 337/73,166 alleles
Filtering AF
0.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.404%
Overall
0.0229%
356/1,551,320 alleles · rare
exomes 173/1,399,014 · genomes 183/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.461% | 217 |
| Remaining individualsnot grpmax-eligible | 0.0183% | 5,463 |
| Admixed American | 0.0157% | 6,369 |
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
- PATL2
- Protein
- p.Pro382=
- Coding
- c.1146C>G
- MANE Select
- NM_001387263
- dbSNP
- rs190933513
- Type
- single nucleotide variant
- Location
- chr15:44669058 (GRCh38)
- Gene constraint
- LOEUF 1.163 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.05
- Residue 382
- a UniProt-annotated variant site (in ozema4; likely pathogenic); a UniProt-annotated variant site (in ozema4)
Disease context
PATL2-related disorder
Similar variants
- PATL2 p.Ala85= Likely benign same condition
- PATL2 p.Asp184= Likely benign same condition
- PATL2 p.Asp231= Likely benign same condition
- PATL2 p.Leu20Pro Benign same condition
- PATL2 p.Phe137= Likely benign same condition
- PATL2 p.Ser143= Likely benign same condition
- PATL2 p.Val272Met Benign same condition
- PATL2 p.Val450Met Likely benign same condition
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/patl2-p-pro382 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown