Is DCX p.Arg102= (c.306T>C) pathogenic?

DCX p.Arg102= (c.306T>C) is classified Likely benign in DCX (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-03). Very rare (popmax 0.00335%, nfe).

How common is DCX p.Arg102= (c.306T>C) in the general population?

DCX p.Arg102= (c.306T>C) is very rare (popmax 0.00335%, nfe) (gnomAD).

DCX p.Arg102=

c.306T>C · rs772189954 · VCV2917140

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00335%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.222	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.57	GERP -4.2, phastCons 0.96
Overall
CADD	7.916	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00335% European (non-Finnish) · 30/895,255 alleles

Filtering AF 0.00238% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00206%

Overall 0.00248% 30/1,209,974 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: DCX
Protein: p.Arg102=
Coding: c.306T>C
MANE Select: NM_001195553
dbSNP: rs772189954
Type: single nucleotide variant
Location: chrX:111410093 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB
Residue 102: the doublecortin 1 domain; a UniProt-annotated variant site (in lisx1)

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

Similar variants

DCX p.Arg102Gly Pathogenic ★ same residue
DCX p.Arg102Ser Pathogenic ★ same residue
DCX p.Arg102Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
DCX p.Arg102His Conflicting classifications of pathogenicity ★ ⚠ 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

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-arg102 (accessed [today's date]).

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