Is DCX p.Val197Met (c.589G>A) pathogenic?

DCX p.Val197Met (c.589G>A) is classified Uncertain significance in DCX (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-18). AlphaMissense: likely pathogenic (0.8999); Absent from gnomAD v4.1; Associated with intellectual disability.

What condition is associated with DCX p.Val197Met (c.589G>A)?

DCX p.Val197Met (c.589G>A) is associated with intellectual disability (ClinVar).

How common is DCX p.Val197Met (c.589G>A) in the general population?

DCX p.Val197Met (c.589G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DCX p.Val197Met (c.589G>A)?

AlphaMissense predicts likely pathogenic (score 0.8999) — an in-silico prediction, not a clinical call.

DCX p.Val197Met

c.589G>A · VCV4074916

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8999 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

intellectual disability

Computational evidence

Protein change
AlphaMissense	0.8999	likely pathogenic
REVEL	0.599	indeterminate
SaProt	LLR -6.98	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP -0.69, phastCons 1
Regional constraint	o/e 0.31	constrained · MANE · 77 kb · p 4.4e-24 · regional, not allelic
Overall
CADD	24.5	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.Val197Met
Coding: c.589G>A
MANE Select: NM_001195553
Type: single nucleotide variant
Location: chrX:111401106 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB
Residue 197: the doublecortin 2 domain; a β-strand

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

Disease context

intellectual disability — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DCX p.Arg344Gln Uncertain significance ★ ⚠ same condition
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
DCX p.Arg178Cys Pathogenic/Likely 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-val197met (accessed [today's date]).

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