NTSR1 p.Arg45=
c.135C>T · rs61742231 · VCV791213
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.57%, afr)
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 -3.7 | GERP -2.4 |
| Overall | ||
| CADD | 3.568 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.57%
African / African-American · 1,924/74,990 alleles
Filtering AF
2.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.43%
Overall
0.142%
2,287/1,609,706 alleles · low-frequency
exomes 1,162/1,457,352 · genomes 1,125/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.57% | 39 |
| Admixed American | 0.232% | 431 |
| Middle Eastern | 0.231% | 432 |
| Remaining individualsnot grpmax-eligible | 0.164% | 611 |
| European (non-Finnish) | 0.00866% | 11,553 |
| South Asian | 0.0066% | 15,144 |
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
- NTSR1
- Protein
- p.Arg45=
- Coding
- c.135C>T
- MANE Select
- NM_002531
- dbSNP
- rs61742231
- Type
- single nucleotide variant
- Location
- chr20:62709342 (GRCh38)
- Gene constraint
- LOEUF 1.261 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.27 · 48 PDB
Similar variants
- NTSR1 c.917-6C>A Benign ★★ same type
- NTSR1 p.Arg388Cys Benign ★★ same type
- NTSR1 p.Gln275His Benign ★★ same type
- NTSR1 p.Gly301= Benign ★★ same type
- NTSR1 p.Ser39= Benign ★★ same type
- NTSR1 p.Tyr339Cys Benign ★★ ⚠ same type
- NTSR1 p.Ala119Val Uncertain significance ★ ⚠ same type
- NTSR1 p.Ala139Pro 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/ntsr1-p-arg45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown