PTCH2 p.Val145=
c.435C>T · rs201198043 · VCV2638782
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00988%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.51 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -4.1 |
| Overall | ||
| CADD | 7.472 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00988%
South Asian · 9/91,080 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00375%
Overall
0.000743%
12/1,614,158 alleles · very rare
exomes 12/1,461,892 · genomes 0/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00988% | 10,120 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,504 |
| European (non-Finnish) | 0.000169% | 590,019 |
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
- PTCH2
- Protein
- p.Val145=
- Coding
- c.435C>T
- MANE Select
- NM_003738
- dbSNP
- rs201198043
- Type
- single nucleotide variant
- Location
- chr1:44832172 (GRCh38)
- Gene constraint
- LOEUF 0.895 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.25
- Residue 145
- the 'extracellular domain 1 (ecd1)' region
Similar variants
- PTCH2 c.2976+2T>C Uncertain significance ★★ same type
- PTCH2 c.526-2A>G Uncertain significance ★★ same type
- PTCH2 c.617+4A>T Uncertain significance ★★ same type
- PTCH2 c.618-6C>A Uncertain significance ★★ same type
- PTCH2 p.Ala1052Thr Uncertain significance ★★ ⚠ same type
- PTCH2 p.Ala1090Val Uncertain significance ★★ ⚠ same type
- PTCH2 p.Ala203Val Uncertain significance ★★ same type
- PTCH2 p.Ala21Thr 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/ptch2-p-val145 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown