Is GRIN2D p.Arg567= (c.1701C>T) pathogenic?

GRIN2D p.Arg567= (c.1701C>T) is classified Likely benign in GRIN2D (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-13). Very rare (popmax 0.00246%, nfe).

How common is GRIN2D p.Arg567= (c.1701C>T) in the general population?

GRIN2D p.Arg567= (c.1701C>T) is very rare (popmax 0.00246%, nfe) (gnomAD).

GRIN2D p.Arg567=

c.1701C>T · rs773742546 · VCV1559951

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00246%, nfe)

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 -0.25	GERP -3.9, phastCons 0.25
Overall
CADD	10.3	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00246% European (non-Finnish) · 29/1,179,990 alleles

Filtering AF 0.00172% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00149%

Overall 0.00459% 74/1,613,888 alleles · very rare exomes 66/1,461,736 · genomes 8/152,152 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0657%	1,523
Remaining individualsnot grpmax-eligible	0.0048%	20,827
European (non-Finnish)grpmax	0.00246%	40,689

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: GRIN2D
Protein: p.Arg567=
Coding: c.1701C>T
MANE Select: NM_000836
dbSNP: rs773742546
Type: single nucleotide variant
Location: chr19:48416121 (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.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
GRIN2D p.Ala1177Thr Uncertain significance ★★ ⚠ same type
GRIN2D p.Ala1208Val 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-arg567 (accessed [today's date]).

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