Is PLCE1 p.Ala577Thr (c.1729G>A) pathogenic?

PLCE1 p.Ala577Thr (c.1729G>A) is classified Conflicting classifications of pathogenicity in PLCE1 (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2026-01-18). AlphaMissense: likely benign (0.0864); Low-frequency (popmax 1.25%, afr); Associated with kidney disorder.

What condition is associated with PLCE1 p.Ala577Thr (c.1729G>A)?

PLCE1 p.Ala577Thr (c.1729G>A) is associated with kidney disorder, nephrotic syndrome, type 3 (ClinVar).

How common is PLCE1 p.Ala577Thr (c.1729G>A) in the general population?

PLCE1 p.Ala577Thr (c.1729G>A) is low-frequency (popmax 1.25%, afr) (gnomAD).

What do computational predictors say about PLCE1 p.Ala577Thr (c.1729G>A)?

AlphaMissense predicts likely benign (score 0.0864) — an in-silico prediction, not a clinical call.

PLCE1 p.Ala577Thr

c.1729G>A · rs141639885 · VCV260713

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.0864 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.25%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

kidney disorder

Computational evidence

Protein change
AlphaMissense	0.0864	likely benign
REVEL	0.078	moderately benign-leaning
SaProt	LLR -5.63	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 8.5	GERP 2.1, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 214 kb · p 0.44 · regional, not allelic
Overall
CADD	21.4	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 1.25% African / African-American · 937/75,058 alleles

Filtering AF 1.18% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.16%

Overall 0.0763% 1,231/1,614,182 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.25%	80
Admixed American	0.253%	395
Middle Eastern	0.115%	866
Remaining individualsnot grpmax-eligible	0.11%	906
European (non-Finnish)	0.00542%	18,438
South Asian	0.0022%	45,541

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.Ala577Thr
Coding: c.1729G>A
MANE Select: NM_016341
dbSNP: rs141639885
Type: single nucleotide variant
Location: chr10:94171416 (GRCh38)
Gene constraint: LOEUF 0.564 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.01 · 3 PDB
Residue 577: the ras-gef domain

Full PLCE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

kidney disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: nephrotic syndrome, type 3

Similar variants

PLCE1 c.4506+1G>A Likely pathogenic ★★ same condition
PLCE1 c.6132+1G>A Likely pathogenic ★★ same condition
PLCE1 p.Arg1246Ter Pathogenic ★★ same condition
PLCE1 p.Arg1434Gln Likely pathogenic ★★ same condition
PLCE1 p.Arg1495Ter Pathogenic/Likely pathogenic ★★ same condition
PLCE1 p.Arg321Ter Pathogenic ★★ same condition
PLCE1 p.Arg493Ter Pathogenic ★★ same condition
PLCE1 p.Gln1020Ter Pathogenic ★★ same condition

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-ala577thr (accessed [today's date]).

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