Is REST p.Asp29Glu (c.87C>A) pathogenic?

REST p.Asp29Glu (c.87C>A) is classified Uncertain significance in REST (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-20). AlphaMissense: likely pathogenic (0.7793); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with REST p.Asp29Glu (c.87C>A)?

REST p.Asp29Glu (c.87C>A) is associated with Inborn genetic diseases (ClinVar).

How common is REST p.Asp29Glu (c.87C>A) in the general population?

REST p.Asp29Glu (c.87C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about REST p.Asp29Glu (c.87C>A)?

AlphaMissense predicts likely pathogenic (score 0.7793) — an in-silico prediction, not a clinical call.

REST p.Asp29Glu

c.87C>A · rs2475797480 · VCV3153125

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7793 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.7793	likely pathogenic
REVEL	0.14	moderately benign-leaning
SaProt	LLR -6.02	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.84	GERP 1.4, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 624 bp · p 0.87 · regional, not allelic
Overall
CADD	20.2	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

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: REST
Protein: p.Asp29Glu
Coding: c.87C>A
MANE Select: NM_005612
dbSNP: rs2475797480
Type: single nucleotide variant
Location: chr4:56910725 (GRCh38)
Gene constraint: LOEUF 0.16 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 49.53 · 3 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

REST p.Asp29Asn Uncertain significance ★ ⚠ same residue
REST p.Ala198Val Uncertain significance ★★ ⚠ same condition
REST p.Ala25Ser Uncertain significance ★★ ⚠ same condition
REST p.Ala642Val Uncertain significance ★★ ⚠ same condition
REST p.Arg199Gly Uncertain significance ★★ ⚠ same condition
REST p.Arg217Cys Uncertain significance ★★ ⚠ same condition
REST p.Asn282Ser Uncertain significance ★★ ⚠ same condition
REST p.Asn390Ser Uncertain significance ★★ ⚠ 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/rest-p-asp29glu (accessed [today's date]).

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