Is GRIN2D p.Pro951= (c.2853G>A) pathogenic?

GRIN2D p.Pro951= (c.2853G>A) is classified Likely benign in GRIN2D (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-04). No allele count reported in gnomAD v4.1 (AN 1,068,004).

How common is GRIN2D p.Pro951= (c.2853G>A) in the general population?

GRIN2D p.Pro951= (c.2853G>A) is no allele count reported in gnomAD v4.1 (AN 1,068,004) (gnomAD).

GRIN2D p.Pro951=

c.2853G>A · rs1971315518 · VCV2839785

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,068,004)

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 -1	GERP -1.4
Overall
CADD	6.738	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,068,004). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: GRIN2D
Protein: p.Pro951=
Coding: c.2853G>A
MANE Select: NM_000836
dbSNP: rs1971315518
Type: single nucleotide variant
Location: chr19:48442779 (GRCh38)
Gene constraint: LOEUF 0.642 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 64.00 · 13 PDB

Full GRIN2D gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GRIN2D p.Pro951Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
GRIN2D p.Pro951Ser Uncertain significance ★ ⚠ same residue
GRIN2D p.Met681Val Pathogenic/Likely pathogenic ★★ same type
GRIN2D p.Val667Ile Pathogenic/Likely pathogenic ★★ same type
GRIN2D p.Ala1032Val Uncertain significance ★★ ⚠ same type
GRIN2D p.Ala1040Thr Uncertain significance ★★ ⚠ same type
GRIN2D p.Ala1085Thr Uncertain significance ★★ ⚠ same type
GRIN2D p.Ala1135Thr 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/grin2d-p-pro951 (accessed [today's date]).

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