Is SGCE p.Ser152= (c.456T>C) pathogenic?

SGCE p.Ser152= (c.456T>C) is classified Likely benign in SGCE (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-23). Very rare (popmax 0.00336%, amr).

How common is SGCE p.Ser152= (c.456T>C) in the general population?

SGCE p.Ser152= (c.456T>C) is very rare (popmax 0.00336%, amr) (gnomAD).

SGCE p.Ser152=

c.456T>C · rs765566124 · VCV741244

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00336%, amr)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.51	GERP -3.2, phastCons 1
Overall
CADD	8.325	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00336% Admixed American · 2/59,542 alleles

Filtering AF 0.000557% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000209%

Overall 0.00019% 3/1,581,908 alleles · very rare exomes 3/1,429,608 · genomes 0/152,300 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00336%	29,771
European (non-Finnish)	8.67e-05%	1,153,031

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: SGCE
Protein: p.Ser152=
Coding: c.456T>C
MANE Select: NM_003919
dbSNP: rs765566124
Type: single nucleotide variant
Location: chr7:94623332 (GRCh38)

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

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/sgce-p-ser152 (accessed [today's date]).

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