NPY2R p.Pro196=
c.588G>A · VCV4559013
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -10 | GERP -3.7 |
| Overall | ||
| CADD | 0.297 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.000929%
15/1,614,026 alleles · ultra-rare
exomes 12/1,461,870 · genomes 3/152,156 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| African / African-American | 0.00667% | 14,985 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| South Asian | 0.0011% | 91,090 |
| European (non-Finnish) | 0.000593% | 168,574 |
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
- NPY2R
- Protein
- p.Pro196=
- Coding
- c.588G>A
- MANE Select
- NM_000910
- Type
- single nucleotide variant
- Location
- chr4:155214527 (GRCh38)
- Gene constraint
- LOEUF 1.079 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.66 · 5 PDB
- Residue 196
- a turn
Similar variants
- NPY2R p.Ala172Thr Benign ★★ same type
- NPY2R p.Arg345Gln Likely benign ★★ same type
- NPY2R p.Leu53= Benign ★★ same type
- NPY2R p.Val218= Benign ★★ same type
- NPY2R p.Ala184Thr Uncertain significance ★ ⚠ same type
- NPY2R p.Ala90Val Uncertain significance ★ ⚠ same type
- NPY2R p.Arg148Gln Uncertain significance ★ ⚠ same type
- NPY2R p.Arg241His 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/npy2r-p-pro196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown