SSTR5 p.Ser11=
c.33C>T · rs35128939 · VCV733020
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.15%, afr)
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 1.6 | GERP 0.1, phastCons 0.94 |
| Overall | ||
| CADD | 6.231 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.15%
African / African-American · 859/74,956 alleles
Filtering AF
1.08%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.06%
Overall
0.0605%
972/1,606,248 alleles · low-frequency
exomes 476/1,453,928 · genomes 496/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.15% | 87 |
| Remaining individualsnot grpmax-eligible | 0.0981% | 1,019 |
| Admixed American | 0.0719% | 1,392 |
| Middle Eastern | 0.0355% | 2,817 |
| South Asian | 0.0011% | 90,704 |
| European (non-Finnish) | 0.000509% | 196,492 |
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
- SSTR5
- Protein
- p.Ser11=
- Coding
- c.33C>T
- MANE Select
- NM_001172560
- dbSNP
- rs35128939
- Type
- single nucleotide variant
- Location
- chr16:1078901 (GRCh38)
- Gene constraint
- LOEUF 1.931 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 81.91 · 7 PDB
- Residue 11
- the 'disordered' region
Similar variants
- SSTR5 p.Thr98Met Uncertain significance ★★ ⚠ same type
- SSTR5 p.Ala161= Benign ★★ same type
- SSTR5 p.Ala231= Benign/Likely benign ★★ same type
- SSTR5 p.Arg240Trp Benign/Likely benign ★★ same type
- SSTR5 p.Leu219= Benign ★★ same type
- SSTR5 p.Leu48Met Benign ★★ same type
- SSTR5 p.Phe107= Benign ★★ same type
- SSTR5 p.Pro335Leu Benign ★★ 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/sstr5-p-ser11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown