PITPNM3 p.Ala884=
c.2652C>T · VCV3650237
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, 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 -11 | GERP -3.9 |
| Overall | ||
| CADD | 0.773 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
South Asian · 10/90,376 alleles
Filtering AF
0.00598%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00456%
Overall
0.00277%
44/1,587,220 alleles · ultra-rare
exomes 44/1,446,754 · genomes 0/140,466 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0111% | 9,038 |
| European (non-Finnish) | 0.00264% | 37,944 |
| Finnishnot grpmax-eligible | 0.00205% | 48,664 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,148 |
| African / African-American | 0.00142% | 70,634 |
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.Ala884=
- Coding
- c.2652C>T
- MANE Select
- NM_031220
- Type
- single nucleotide variant
- Location
- chr17:6455611 (GRCh38)
- Gene constraint
- LOEUF 0.354 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.73 · 1 PDB
- Residue 884
- the lns2 domain
Similar variants
- 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
- PITPNM3 c.*3462G>C Uncertain significance ★★ same type
- PITPNM3 p.Ala288Ser 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-ala884 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown