Is DCX p.Arg258Cys (c.772C>T) pathogenic?

DCX p.Arg258Cys (c.772C>T) is classified Conflicting classifications of pathogenicity in DCX (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2024-03-24). AlphaMissense: likely pathogenic (0.9376); Absent from gnomAD v4.1.

How common is DCX p.Arg258Cys (c.772C>T) in the general population?

DCX p.Arg258Cys (c.772C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DCX p.Arg258Cys (c.772C>T)?

AlphaMissense predicts likely pathogenic (score 0.9376) — an in-silico prediction, not a clinical call.

DCX p.Arg258Cys

c.772C>T · rs727503897 · VCV166990

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9376 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9376	likely pathogenic
REVEL	0.906	moderately pathogenic-leaning
SaProt	LLR -12.80	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 2.1, phastCons 1
Regional constraint	o/e 0.31	constrained · MANE · 77 kb · p 4.4e-24 · regional, not allelic
Overall
CADD	29.2	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DCX
Protein: p.Arg258Cys
Coding: c.772C>T
MANE Select: NM_001195553
dbSNP: rs727503897
Type: single nucleotide variant
Location: chrX:111333087 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB
Residue 258: the doublecortin 2 domain

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

Similar variants

DCX p.Arg258Pro Likely pathogenic ★ same residue
DCX p.Arg258= Likely benign ★ same residue
DCX c.364+1G>A Likely pathogenic ★★ same type
DCX c.705+1G>A Pathogenic ★★ same type
DCX c.706-2A>G Pathogenic ★★ same type
DCX c.809-1G>A Pathogenic/Likely pathogenic ★★ same type
DCX p.Ala204Asp Pathogenic ★★ same type
DCX p.Ala251Ser Pathogenic ★★ 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/dcx-p-arg258cys (accessed [today's date]).

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