Is DCX p.Asn317= (c.951C>T) pathogenic?

DCX p.Asn317= (c.951C>T) is classified Likely benign in DCX (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-01-24). Very rare (popmax 0.00889%, eas); Associated with Inborn genetic diseases.

What condition is associated with DCX p.Asn317= (c.951C>T)?

DCX p.Asn317= (c.951C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DCX p.Asn317= (c.951C>T) in the general population?

DCX p.Asn317= (c.951C>T) is very rare (popmax 0.00889%, eas) (gnomAD).

DCX p.Asn317=

c.951C>T · rs1204976259 · VCV787302

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00889%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.169	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP -4.1, phastCons 1
Overall
CADD	2.766	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00889% East Asian · 3/33,740 alleles

Filtering AF 0.00236% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00141%

Overall 0.00174% 21/1,209,172 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00889%	11,247
South Asian	0.00705%	14,184
Remaining individualsnot grpmax-eligible	0.00421%	23,780
African / African-American	0.00351%	28,491
Finnishnot grpmax-eligible	0.00215%	46,606
European (non-Finnish)	0.00101%	99,421

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.Asn317=
Coding: c.951C>T
MANE Select: NM_001195553
dbSNP: rs1204976259
Type: single nucleotide variant
Location: chrX:111312732 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB
Residue 317: 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-asn317 (accessed [today's date]).

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