PITPNM3 p.Pro147=
c.441G>A · rs539664590 · VCV1165029
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.136%, sas)
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 -20 | |
| Overall | ||
| CADD | 1.652 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.136%
South Asian · 124/90,964 alleles
Filtering AF
0.117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.109%
Overall
0.0106%
171/1,612,264 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.136% | 734 |
| Middle Eastern | 0.0165% | 6,054 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,811 |
| East Asian | 0.00671% | 14,899 |
| African / African-American | 0.00538% | 18,587 |
| Admixed American | 0.00334% | 29,942 |
| European (non-Finnish) | 0.00246% | 40,669 |
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
- PITPNM3
- Protein
- p.Pro147=
- Coding
- c.441G>A
- MANE Select
- NM_031220
- dbSNP
- rs539664590
- Type
- single nucleotide variant
- Location
- chr17:6483663 (GRCh38)
- Gene constraint
- LOEUF 0.354 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.73 · 1 PDB
- Residue 147
- an α-helix
Similar variants
- PITPNM3 p.Pro147Leu Uncertain significance ★★ ⚠ same residue
- PITPNM3 p.Pro147Ser Uncertain significance ★ ⚠ same residue
- PITPNM3 c.2306+6T>A Uncertain significance ★★ same type
- PITPNM3 c.351+3A>C Uncertain significance ★★ same type
- PITPNM3 c.351+5G>A Uncertain significance ★★ same type
- PITPNM3 c.*2957G>A Uncertain significance ★★ same type
- PITPNM3 c.*3446G>T Uncertain significance ★★ same type
- PITPNM3 c.*3452C>G 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/pitpnm3-p-pro147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown