Is GABBR2 p.Pro30= (c.90G>T) pathogenic?

GABBR2 p.Pro30= (c.90G>T) is classified Likely benign in GABBR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-28). Ultra-rare (popmax 0.0141%, afr); Associated with Epileptic encephalopathy.

What condition is associated with GABBR2 p.Pro30= (c.90G>T)?

GABBR2 p.Pro30= (c.90G>T) is associated with Epileptic encephalopathy (ClinVar).

How common is GABBR2 p.Pro30= (c.90G>T) in the general population?

GABBR2 p.Pro30= (c.90G>T) is ultra-rare (popmax 0.0141%, afr) (gnomAD).

GABBR2 p.Pro30=

c.90G>T · rs1039627589 · VCV1161680

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0141%, afr)

Conditions

Epileptic encephalopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.5	GERP 0.084, phastCons 1
Overall
CADD	9.364	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0141% African / African-American · 9/63,612 alleles

Filtering AF 0.00733% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0055%

Overall 0.000806% 10/1,240,198 alleles · ultra-rare exomes 1/1,090,128 · genomes 9/150,070 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0141%	7,068
Admixed American	0.00427%	23,404

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: GABBR2
Protein: p.Pro30=
Coding: c.90G>T
MANE Select: NM_005458
dbSNP: rs1039627589
Type: single nucleotide variant
Location: chr9:98708648 (GRCh38)
Gene constraint: LOEUF 0.394 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 78.00 · 26 PDB

Full GABBR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Epileptic encephalopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GABBR2 p.Pro30Gln Uncertain significance ★ ⚠ same residue
GABBR2 p.Pro30Leu Uncertain significance ★ ⚠ same residue
GABBR2 p.Pro30_Leu31insPro Uncertain significance ★ same residue
GABBR2 p.Gly693Trp Pathogenic ★★ same condition
GABBR2 p.Ala444Thr Uncertain significance ★★ ⚠ same condition
GABBR2 p.Ala580Ser Uncertain significance ★★ ⚠ same condition
GABBR2 p.Ala69Pro Uncertain significance ★★ ⚠ same condition
GABBR2 p.Ala708Ser 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/gabbr2-p-pro30 (accessed [today's date]).

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