Is DCDC2 p.Gly54= (c.162C>T) pathogenic?

DCDC2 p.Gly54= (c.162C>T) is classified Likely benign in DCDC2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-04-18). Very rare (popmax 8.47e-05%, nfe); Associated with DCDC2-related disorder.

What condition is associated with DCDC2 p.Gly54= (c.162C>T)?

DCDC2 p.Gly54= (c.162C>T) is associated with DCDC2-related disorder (ClinVar).

How common is DCDC2 p.Gly54= (c.162C>T) in the general population?

DCDC2 p.Gly54= (c.162C>T) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

DCDC2 p.Gly54=

c.162C>T · rs2532474604 · VCV3048480

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

DCDC2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.022	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	GERP -2, phastCons 1
Overall
CADD	16.72	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,036 alleles

Overall 6.84e-05% 1/1,461,158 alleles · very rare

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: DCDC2
Protein: p.Gly54=
Coding: c.162C>T
MANE Select: NM_016356
dbSNP: rs2532474604
Type: single nucleotide variant
Location: chr6:24357589 (GRCh38)
Gene constraint: LOEUF 1.062 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.93 · 1 PDB
Residue 54: the doublecortin 1 domain

Full DCDC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DCDC2-related disorder

Similar variants

DCDC2 p.Gly54Arg Uncertain significance ★ ⚠ same residue
DCDC2 c.705-2A>G Pathogenic ★★ same condition
DCDC2 c.557+1G>T Pathogenic ★ same condition
DCDC2 p.Gln448Lys Uncertain significance ★ ⚠ same condition
DCDC2 p.Gln417Ter Likely pathogenic same condition
DCDC2 p.Gly368Glu Uncertain significance ⚠ same condition
DCDC2 p.Lys249Gln Uncertain significance ⚠ same condition
DCDC2 c.1326+6T>G 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/dcdc2-p-gly54 (accessed [today's date]).

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