Is SSTR2 p.Ala4Val (c.11C>T) pathogenic?

SSTR2 p.Ala4Val (c.11C>T) is classified Likely benign in SSTR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-30). AlphaMissense: likely benign (0.134); Very rare (popmax 0.00401%, afr).

How common is SSTR2 p.Ala4Val (c.11C>T) in the general population?

SSTR2 p.Ala4Val (c.11C>T) is very rare (popmax 0.00401%, afr) (gnomAD).

What do computational predictors say about SSTR2 p.Ala4Val (c.11C>T)?

AlphaMissense predicts likely benign (score 0.134) — an in-silico prediction, not a clinical call.

SSTR2 p.Ala4Val

c.11C>T · VCV3449872

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.134 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00401%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.134	likely benign
REVEL	0.082	moderately benign-leaning
SaProt	LLR -6.93	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.8
Regional constraint	o/e 0.99	unconstrained · MANE · 186 bp · p 0.96 · regional, not allelic
Overall
CADD	0.237	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 0.00401% African / African-American · 3/74,888 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000495%

Overall 0.000931% 15/1,611,512 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00401%	24,963
South Asian	0.00221%	45,347
Admixed American	0.00167%	59,772
Remaining individualsnot grpmax-eligible	0.0016%	62,366
European (non-Finnish)	0.000678%	147,386

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: SSTR2
Protein: p.Ala4Val
Coding: c.11C>T
MANE Select: NM_001050
Type: single nucleotide variant
Location: chr17:73169330 (GRCh38)
Gene constraint: LOEUF 0.756 · pLI 0.14 (gnomAD)
Structure: AlphaFold pLDDT 81.75 · 17 PDB

Full SSTR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SSTR2 p.Ala181Val Uncertain significance ★ ⚠ same type
SSTR2 p.Arg157Gln Uncertain significance ★ ⚠ same type
SSTR2 p.Arg184Gln Uncertain significance ★ ⚠ same type
SSTR2 p.Arg340Gln Uncertain significance ★ ⚠ same type
SSTR2 p.Asn22Ser Uncertain significance ★ ⚠ same type
SSTR2 p.Asn318Ser Uncertain significance ★ ⚠ same type
SSTR2 p.Asn325Lys Uncertain significance ★ ⚠ same type
SSTR2 p.Asn9Ser 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/sstr2-p-ala4val (accessed [today's date]).

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