NTSR2 p.Arg64=
c.192C>A · rs11556847 · VCV2650687
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.238%, nfe)
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 -0.097 | GERP -2.9 |
| Overall | ||
| CADD | 3.879 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.238%
European (non-Finnish) · 2,719/1,140,062 alleles
Filtering AF
0.231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.228%
Overall
0.191%
2,896/1,518,268 alleles · rare
exomes 2,714/1,366,092 · genomes 182/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.238% | 419 |
| Remaining individualsnot grpmax-eligible | 0.167% | 601 |
| Admixed American | 0.0669% | 1,496 |
| Finnishnot grpmax-eligible | 0.0518% | 1,932 |
| African / African-American | 0.0282% | 3,543 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0037% | 27,058 |
| South Asian | 0.00247% | 40,412 |
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
- NTSR2
- Protein
- p.Arg64=
- Coding
- c.192C>A
- MANE Select
- NM_012344
- dbSNP
- rs11556847
- Type
- single nucleotide variant
- Location
- chr2:11669938 (GRCh38)
- Gene constraint
- LOEUF 1.731 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.25
Similar variants
- NTSR2 p.Arg64Leu Uncertain significance ★ ⚠ same residue
- NTSR2 p.Arg282Lys Benign ★★ same type
- NTSR2 p.Ala190Thr Uncertain significance ★ ⚠ same type
- NTSR2 p.Ala327Val Uncertain significance ★ ⚠ same type
- NTSR2 p.Ala360Thr Uncertain significance ★ ⚠ same type
- NTSR2 p.Ala47Val Uncertain significance ★ ⚠ same type
- NTSR2 p.Ala62Thr Uncertain significance ★ ⚠ same type
- NTSR2 p.Ala65Thr 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/ntsr2-p-arg64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown