Is SSTR5 p.Val121Ile (c.361G>A) pathogenic?

SSTR5 p.Val121Ile (c.361G>A) is classified Likely benign in SSTR5 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-13). AlphaMissense: likely benign (0.0826); Very rare (popmax 0.00975%, nfe).

How common is SSTR5 p.Val121Ile (c.361G>A) in the general population?

SSTR5 p.Val121Ile (c.361G>A) is very rare (popmax 0.00975%, nfe) (gnomAD).

What do computational predictors say about SSTR5 p.Val121Ile (c.361G>A)?

AlphaMissense predicts likely benign (score 0.0826) — an in-silico prediction, not a clinical call.

SSTR5 p.Val121Ile

c.361G>A · rs753466942 · VCV2372907

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0826 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00975%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0826	likely benign
REVEL	0.032	moderately benign-leaning
SaProt	LLR -7.53	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.18	GERP -2.5
Regional constraint	o/e 0.95	unconstrained · MANE · 1,091 bp · p 0.24 · regional, not allelic
Overall
CADD	11.87	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00975% European (non-Finnish) · 115/1,179,904 alleles

Filtering AF 0.00826% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00774%

Overall 0.00781% 126/1,612,344 alleles · very rare exomes 108/1,460,110 · genomes 18/152,234 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00975%	10,260
African / African-American	0.00934%	10,703
Remaining individualsnot grpmax-eligible	0.0048%	20,816
Admixed American	0.00167%	60,010

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.Val121Ile
Coding: c.361G>A
MANE Select: NM_001172560
dbSNP: rs753466942
Type: single nucleotide variant
Location: chr16:1079229 (GRCh38)
Gene constraint: LOEUF 1.931 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 81.91 · 7 PDB
Residue 121: an α-helix

Full SSTR5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-val121ile (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown