Is DCX p.Cys35Arg (c.103T>C) pathogenic?

DCX p.Cys35Arg (c.103T>C) is classified Uncertain significance in DCX (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-04-29). AlphaMissense: likely pathogenic (0.9977); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DCX p.Cys35Arg (c.103T>C)?

DCX p.Cys35Arg (c.103T>C) is associated with Inborn genetic diseases (ClinVar).

How common is DCX p.Cys35Arg (c.103T>C) in the general population?

DCX p.Cys35Arg (c.103T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DCX p.Cys35Arg (c.103T>C)?

AlphaMissense predicts likely pathogenic (score 0.9977) — an in-silico prediction, not a clinical call.

DCX p.Cys35Arg

c.103T>C · rs945410935 · VCV1712796

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9977 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9977	likely pathogenic
REVEL	0.447	indeterminate
SaProt	LLR -13.66	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 0.91, phastCons 1
Regional constraint	o/e 0.31	constrained · MANE · 77 kb · p 4.4e-24 · regional, not allelic
Overall
CADD	25.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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.Cys35Arg
Coding: c.103T>C
MANE Select: NM_001195553
dbSNP: rs945410935
Type: single nucleotide variant
Location: chrX:111410296 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DCX p.Arg196His Pathogenic/Likely pathogenic ★★ same condition
DCX p.Arg39Ter Pathogenic ★★ same condition
DCX p.Ala295Thr Uncertain significance ★★ ⚠ same condition
DCX p.Ile107Thr Uncertain significance ★★ ⚠ same condition
DCX c.706-4A>G Benign/Likely benign ★★ same condition
DCX p.Ala286Ser Benign/Likely benign ★★ same condition
DCX p.Ala316= Benign/Likely benign ★★ same condition
DCX p.Arg196= Benign/Likely benign ★★ 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/dcx-p-cys35arg (accessed [today's date]).

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