Is SSTR3 p.Pro196= (c.588C>T) pathogenic?

SSTR3 p.Pro196= (c.588C>T) is classified Likely benign in SSTR3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-27). Very rare (popmax 0.00713%, nfe).

How common is SSTR3 p.Pro196= (c.588C>T) in the general population?

SSTR3 p.Pro196= (c.588C>T) is very rare (popmax 0.00713%, nfe) (gnomAD).

SSTR3 p.Pro196=

c.588C>T · VCV3801875

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00713%, nfe)

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 -14	GERP -3.8
Overall
CADD	0.249	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00713% European (non-Finnish) · 84/1,178,466 alleles

Filtering AF 0.00588% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00542%

Overall 0.00547% 88/1,609,442 alleles · very rare exomes 85/1,457,290 · genomes 3/152,152 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00713%	14,029
Remaining individualsnot grpmax-eligible	0.00322%	31,102
African / African-American	0.00267%	37,409

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: SSTR3
Protein: p.Pro196=
Coding: c.588C>T
MANE Select: NM_001051
Type: single nucleotide variant
Location: chr22:37207216 (GRCh38)
Gene constraint: LOEUF 1.881 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 74.90 · 3 PDB

Full SSTR3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SSTR3 p.Ala157Pro Uncertain significance ★ ⚠ same type
SSTR3 p.Ala170Val Uncertain significance ★ ⚠ same type
SSTR3 p.Ala172Val Uncertain significance ★ ⚠ same type
SSTR3 p.Ala200Val Uncertain significance ★ ⚠ same type
SSTR3 p.Ala264Val Uncertain significance ★ ⚠ same type
SSTR3 p.Ala74Asp Uncertain significance ★ ⚠ same type
SSTR3 p.Arg150Cys Uncertain significance ★ ⚠ same type
SSTR3 p.Arg153Cys 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/sstr3-p-pro196 (accessed [today's date]).

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