Is SSTR5 p.Ser103Phe (c.308C>T) pathogenic?

SSTR5 p.Ser103Phe (c.308C>T) is classified Uncertain significance in SSTR5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-08). AlphaMissense: ambiguous (0.3956); Very rare (popmax 0.00133%, afr).

How common is SSTR5 p.Ser103Phe (c.308C>T) in the general population?

SSTR5 p.Ser103Phe (c.308C>T) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about SSTR5 p.Ser103Phe (c.308C>T)?

AlphaMissense predicts ambiguous (score 0.3956) — an in-silico prediction, not a clinical call.

SSTR5 p.Ser103Phe

c.308C>T · rs1201637702 · VCV2617137

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3956 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.3956	ambiguous
REVEL	0.255	benign-leaning
SaProt	LLR -4.32	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 5.9	GERP 0.57, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 1,091 bp · p 0.24 · regional, not allelic
Overall
CADD	24.0	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 0.00133% African / African-American · 1/74,938 alleles

Overall 6.2e-05% 1/1,612,468 alleles · very rare exomes 0/1,460,208 · genomes 1/152,260 · joint denominator

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.Ser103Phe
Coding: c.308C>T
MANE Select: NM_001172560
dbSNP: rs1201637702
Type: single nucleotide variant
Location: chr16:1079176 (GRCh38)
Gene constraint: LOEUF 1.931 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 81.91 · 7 PDB

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-ser103phe (accessed [today's date]).

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