Is CGB7 p.Ser152Phe (c.455C>T) pathogenic?

CGB7 p.Ser152Phe (c.455C>T) is classified Uncertain significance in CGB7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-27). AlphaMissense: likely benign (0.1524); Absent from gnomAD v4.1.

How common is CGB7 p.Ser152Phe (c.455C>T) in the general population?

CGB7 p.Ser152Phe (c.455C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CGB7 p.Ser152Phe (c.455C>T)?

AlphaMissense predicts likely benign (score 0.1524) — an in-silico prediction, not a clinical call.

CGB7 p.Ser152Phe

c.455C>T · rs775808413 · VCV2339393

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1524 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1524	likely benign
REVEL	0.043	moderately benign-leaning
SaProt	LLR -9.25	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 0.073
Regional constraint	o/e 1.08	unconstrained · MANE · 40 bp · p 0.72 · regional, not allelic
Overall
CADD	14.49	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: CGB7
Protein: p.Ser152Phe
Coding: c.455C>T
MANE Select: NM_001385261
dbSNP: rs775808413
Type: single nucleotide variant
Location: chr19:49054334 (GRCh38)
Gene constraint: LOEUF 1.838 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.70
Residue 152: the 'disordered' region

Full CGB7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CGB7 p.Ser152Tyr Uncertain significance ★ ⚠ same residue
CGB7 p.Ala103Thr Uncertain significance ★ ⚠ same type
CGB7 p.Arg115His Uncertain significance ★ ⚠ same type
CGB7 p.Arg30His Uncertain significance ★ ⚠ same type
CGB7 p.Arg30Pro Uncertain significance ★ ⚠ same type
CGB7 p.Arg63Cys Uncertain significance ★ ⚠ same type
CGB7 p.Arg80Gly Uncertain significance ★ ⚠ same type
CGB7 p.Arg80His 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/cgb7-p-ser152phe (accessed [today's date]).

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