Is GABRE p.Lys451Arg (c.1352A>G) pathogenic?

GABRE p.Lys451Arg (c.1352A>G) is classified Uncertain significance in GABRE (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-09). AlphaMissense: likely benign (0.0639); Very rare (popmax 0.000223%, nfe).

How common is GABRE p.Lys451Arg (c.1352A>G) in the general population?

GABRE p.Lys451Arg (c.1352A>G) is very rare (popmax 0.000223%, nfe) (gnomAD).

What do computational predictors say about GABRE p.Lys451Arg (c.1352A>G)?

AlphaMissense predicts likely benign (score 0.0639) — an in-silico prediction, not a clinical call.

GABRE p.Lys451Arg

c.1352A>G · VCV3852469

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0639 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000223%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0639	likely benign
REVEL	0.096	moderately benign-leaning
SaProt	LLR -5.66	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 -0.72	GERP 1.6
Regional constraint	o/e 1.02	unconstrained · MANE · 20 kb · p 0.65 · regional, not allelic
Overall
CADD	0.07	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

Grpmax group 0.000223% European (non-Finnish) · 2/895,491 alleles

Filtering AF 3.7e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.4e-05%

Overall 0.000182% 2/1,097,999 alleles · very rare

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: GABRE
Protein: p.Lys451Arg
Coding: c.1352A>G
MANE Select: NM_004961
Type: single nucleotide variant
Location: chrX:151954870 (GRCh38)
Structure: AlphaFold pLDDT 73.13

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

Similar variants

GABRE p.Lys451Asn Uncertain significance ★ ⚠ same residue
GABRE p.Arg176His Uncertain significance ★★ ⚠ same type
GABRE p.Asn134= Likely benign ★★ same type
GABRE p.Glu435Asp Benign ★★ same type
GABRE p.Gly62= Benign ★★ same type
GABRE p.Leu323= Benign ★★ same type
GABRE p.Ser102Ala Benign ★★ same type
GABRE p.Ala193Gly 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/gabre-p-lys451arg (accessed [today's date]).

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