Is DCX p.Pro27= (c.81T>G) pathogenic?

DCX p.Pro27= (c.81T>G) is classified Likely benign in DCX (ClinVar, Single submitter, 1 submitter; last evaluated 2017-06-28). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DCX p.Pro27= (c.81T>G)?

DCX p.Pro27= (c.81T>G) is associated with Inborn genetic diseases (ClinVar).

How common is DCX p.Pro27= (c.81T>G) in the general population?

DCX p.Pro27= (c.81T>G) is absent from gnomAD v4.1 (gnomAD).

DCX p.Pro27=

c.81T>G · rs2524859792 · VCV1762439

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.144	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.4	GERP -4.2, phastCons 0.003
Overall
CADD	2.808	PHRED · no single calibrated threshold — expert panels disagree

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.Pro27=
Coding: c.81T>G
MANE Select: NM_001195553
dbSNP: rs2524859792
Type: single nucleotide variant
Location: chrX:111410318 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB
Residue 27: the 'disordered' region

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.Cys35Arg 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

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-pro27 (accessed [today's date]).

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