DCX p.Tyr64Ter
c.192C>G · rs764964209 · VCV489234
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 7 |
| REVEL | 0.3 | indeterminate |
| Splicing | ||
| SpliceAI | Δ0.34 | acceptor gain · deltas |
| Pangolin | Δ0.36 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 9.9 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 43.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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.Tyr64Ter
- Coding
- c.192C>G
- MANE Select
- NM_001195553
- dbSNP
- rs764964209
- Type
- single nucleotide variant
- Location
- chrX:111410207 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
- Residue 64
- the doublecortin 1 domain
Similar variants
- DCX p.Tyr64Asn Likely pathogenic ★ same residue
- DCX p.Tyr64Asp Pathogenic ★ same residue
- DCX p.Tyr64Cys Likely pathogenic ★ 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
- DCX p.Ala204Asp 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-tyr64ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown