DCPS c.201+2T>C
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Al-Raqad syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +2 | canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone |
| SpliceAI | Δ0.94 | donor loss · deltas |
| Pangolin | Δ0.55 | loss · gain 0.19 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 6.2 | GERP 2.2, phastCons 1 |
| Non-coding constraint | Z 3.51 | 1 kb window · o/e 0.77 · regional · uncalibrated |
| Overall | ||
| CADD | 30.0 | 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
- DCPS
- Coding
- c.201+2T>C
- MANE Select
- NM_014026
- dbSNP
- rs1057519083
- Type
- single nucleotide variant
- Location
- chr11:126304283 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.18 · 11 PDB
Similar variants
- DCPS p.Arg152Ter Likely pathogenic ★★ same condition
- DCPS p.Ala184Thr Uncertain significance ★★ ⚠ same condition
- DCPS p.Pro235Leu Uncertain significance ★★ ⚠ same condition
- DCPS p.Gln105= Benign ★★ same condition
- DCPS p.Phe63= Benign ★★ same condition
- DCPS c.201+1G>T Likely pathogenic ★ same condition
- DCPS p.Glu286Ter Likely pathogenic ★ same condition
- DCPS c.201+4C>G Uncertain significance ★ 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/dcps-c-201-plus-2t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown