Is GRIN2A p.Pro13Arg (c.38C>G) pathogenic?

GRIN2A p.Pro13Arg (c.38C>G) is classified Uncertain significance in GRIN2A (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-18). AlphaMissense: ambiguous (0.4627); Very rare (popmax 8.48e-05%, nfe); Associated with Landau-Kleffner syndrome.

What condition is associated with GRIN2A p.Pro13Arg (c.38C>G)?

GRIN2A p.Pro13Arg (c.38C>G) is associated with Landau-Kleffner syndrome (ClinVar).

How common is GRIN2A p.Pro13Arg (c.38C>G) in the general population?

GRIN2A p.Pro13Arg (c.38C>G) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

How is Landau-Kleffner syndrome inherited?

Typically Autosomal dominant, Unknown (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about GRIN2A p.Pro13Arg (c.38C>G)?

AlphaMissense predicts ambiguous (score 0.4627) — an in-silico prediction, not a clinical call.

GRIN2A p.Pro13Arg

c.38C>G · rs367543131 · VCV1469062

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4627 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

Landau-Kleffner syndrome

Computational evidence

Protein change
AlphaMissense	0.4627	ambiguous
REVEL	0.168	moderately benign-leaning
SaProt	LLR -7.36	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.4	GERP 0.39, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 371 bp · p 0.025 · regional, not allelic
Overall
CADD	22.4	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 8.48e-05% European (non-Finnish) · 1/1,179,848 alleles

Overall 6.22e-05% 1/1,607,868 alleles · very rare exomes 1/1,455,550 · genomes 0/152,318 · joint denominator

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: GRIN2A
Protein: p.Pro13Arg
Coding: c.38C>G
MANE Select: NM_001134407
dbSNP: rs367543131
Type: single nucleotide variant
Location: chr16:10180374 (GRCh38)
Gene constraint: LOEUF 0.268 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 60.70 · 37 PDB

Full GRIN2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Landau-Kleffner syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Landau-Kleffner syndrome (Orphanet):

Inheritance: Autosomal dominant, Unknown
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Japan)

Similar variants

GRIN2A p.Pro13= Likely benign ★★ same residue
GRIN2A p.Pro13Leu Likely benign ★★ same residue
GRIN2A c.1007+1G>A Pathogenic/Likely pathogenic ★★ same condition
GRIN2A c.1007+1G>T Pathogenic ★★ same condition
GRIN2A c.1123-2A>G Pathogenic/Likely pathogenic ★★ same condition
GRIN2A c.1497+1G>T Pathogenic/Likely pathogenic ★★ same condition
GRIN2A c.2007+1G>T Likely pathogenic ★★ same condition
GRIN2A c.2168+1G>C Pathogenic/Likely 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/grin2a-p-pro13arg (accessed [today's date]).

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