SSTR4 p.Ser253=
c.759G>A · rs138321784 · VCV737282
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.13%, 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 -5.3 | GERP -3.8 |
| Overall | ||
| CADD | 4.677 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.13%
African / African-American · 850/75,058 alleles
Filtering AF
1.07%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.04%
Overall
0.0603%
973/1,614,118 alleles · low-frequency
exomes 511/1,461,826 · genomes 462/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.13% | 88 |
| Remaining individualsnot grpmax-eligible | 0.0704% | 1,421 |
| Admixed American | 0.06% | 1,668 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.0033% | 30,257 |
| South Asian | 0.0022% | 45,540 |
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
- SSTR4
- Protein
- p.Ser253=
- Coding
- c.759G>A
- MANE Select
- NM_001052
- dbSNP
- rs138321784
- Type
- single nucleotide variant
- Location
- chr20:23036242 (GRCh38)
- Structure
- AlphaFold pLDDT 78.72 · 2 PDB
- Residue 253
- an α-helix
Similar variants
- SSTR4 p.Ser253Trp Uncertain significance ★ same residue
- SSTR4 p.Leu233= Benign ★★ same type
- SSTR4 p.Thr17= Benign ★★ same type
- SSTR4 p.Val210= Benign ★★ same type
- SSTR4 p.Ala155Val Uncertain significance ★ ⚠ same type
- SSTR4 p.Ala18Thr Uncertain significance ★ ⚠ same type
- SSTR4 p.Ala240Val Uncertain significance ★ ⚠ same type
- SSTR4 p.Ala28Ser 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/sstr4-p-ser253 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown