Is SSTR1 p.Pro350Ser (c.1048C>T) pathogenic?

SSTR1 p.Pro350Ser (c.1048C>T) is classified Uncertain significance in SSTR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-12). AlphaMissense: likely benign (0.3137); Absent from gnomAD v4.1.

How common is SSTR1 p.Pro350Ser (c.1048C>T) in the general population?

SSTR1 p.Pro350Ser (c.1048C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SSTR1 p.Pro350Ser (c.1048C>T)?

AlphaMissense predicts likely benign (score 0.3137) — an in-silico prediction, not a clinical call.

SSTR1 p.Pro350Ser

c.1048C>T · VCV3962573

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3137 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3137	likely benign
REVEL	0.16	moderately benign-leaning
SaProt	LLR -5.86	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 7.7	GERP 1.8, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 621 bp · p 0.72 · regional, not allelic
Overall
CADD	25.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SSTR1
Protein: p.Pro350Ser
Coding: c.1048C>T
MANE Select: NM_001049
Type: single nucleotide variant
Location: chr14:38210437 (GRCh38)
Gene constraint: LOEUF 0.808 · pLI 0.08 (gnomAD)
Structure: AlphaFold pLDDT 79.74 · 4 PDB

Full SSTR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SSTR1 p.Val136= Benign ★★ same type
SSTR1 p.Ala297Val Uncertain significance ★ ⚠ same type
SSTR1 p.Ala357Gly Uncertain significance ★ ⚠ same type
SSTR1 p.Arg264Cys Uncertain significance ★ ⚠ same type
SSTR1 p.Arg264Gly Uncertain significance ★ ⚠ same type
SSTR1 p.Arg336Ser Uncertain significance ★ ⚠ same type
SSTR1 p.Arg380His Uncertain significance ★ ⚠ same type
SSTR1 p.Arg380Pro 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/sstr1-p-pro350ser (accessed [today's date]).

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