Is DDRGK1 p.Arg152= (c.456C>T) pathogenic?

DDRGK1 p.Arg152= (c.456C>T) is classified Likely benign in DDRGK1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-21). Very rare (popmax 0.00834%, amr).

How common is DDRGK1 p.Arg152= (c.456C>T) in the general population?

DDRGK1 p.Arg152= (c.456C>T) is very rare (popmax 0.00834%, amr) (gnomAD).

DDRGK1 p.Arg152=

c.456C>T · rs201354562 · VCV2883666

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00834%, amr)

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 -0.35	GERP -4.6, phastCons 0.001
Overall
CADD	3.954	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00834% Admixed American · 5/59,984 alleles

Filtering AF 0.00323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00207%

Overall 0.000867% 14/1,613,834 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00834%	11,997
African / African-American	0.00666%	15,006
Finnishnot grpmax-eligible	0.00157%	63,856
European (non-Finnish)	0.000254%	393,326

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: DDRGK1
Protein: p.Arg152=
Coding: c.456C>T
MANE Select: NM_023935
dbSNP: rs201354562
Type: single nucleotide variant
Location: chr20:3200055 (GRCh38)
Gene constraint: LOEUF 1.213 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.52 · 8 PDB
Residue 152: an α-helix; the 'disordered' region; the 'mediates interaction with trip4' region

Full DDRGK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DDRGK1 p.Arg152Cys Uncertain significance ★ ⚠ same residue
DDRGK1 p.Arg152His Uncertain significance ★ ⚠ same residue
DDRGK1 p.Arg131Ter Pathogenic ★★ same type
DDRGK1 p.Ala29Val Uncertain significance ★★ ⚠ same type
DDRGK1 p.Ala95Gly Uncertain significance ★★ ⚠ same type
DDRGK1 p.Arg147Gln Uncertain significance ★★ ⚠ same type
DDRGK1 p.Arg241His Uncertain significance ★★ ⚠ same type
DDRGK1 p.Arg265Trp 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/ddrgk1-p-arg152 (accessed [today's date]).

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