Is PLCE1 p.Arg2157= (c.6471C>T) pathogenic?

PLCE1 p.Arg2157= (c.6471C>T) is classified Likely benign in PLCE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-20). Rare (popmax 0.181%, mid).

How common is PLCE1 p.Arg2157= (c.6471C>T) in the general population?

PLCE1 p.Arg2157= (c.6471C>T) is rare (popmax 0.181%, mid) (gnomAD).

PLCE1 p.Arg2157=

c.6471C>T · rs776074916 · VCV2901453

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.181%, mid)

⚠ 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 -20	GERP -4.7
Overall
CADD	0.853	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.181% Middle Eastern · 11/6,082 alleles

Filtering AF 0.101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0784%

Overall 0.00533% 86/1,614,002 alleles · rare exomes 82/1,461,826 · genomes 4/152,176 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.181%	553
South Asian	0.00878%	11,385
Remaining individualsnot grpmax-eligible	0.008%	12,498
European (non-Finnish)	0.00517%	19,344
East Asian	0.00223%	44,890

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: PLCE1
Protein: p.Arg2157=
Coding: c.6471C>T
MANE Select: NM_016341
dbSNP: rs776074916
Type: single nucleotide variant
Location: chr10:94322029 (GRCh38)

Full PLCE1 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/plce1-p-arg2157 (accessed [today's date]).

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