GPATCH11 c.449+1G>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
Early onset and severe retinal dystrophy with neurological impairment and facial dysmorphia
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 +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | Δ1.00 | donor loss · deltas |
| Pangolin | Δ0.88 | loss · gain 0.64 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 35.0 | 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
- GPATCH11
- Coding
- c.449+1G>C
- MANE Select
- NM_174931
- dbSNP
- rs770171252
- Type
- single nucleotide variant
- Location
- chr2:37092037 (GRCh38)
- Gene constraint
- LOEUF 1.008 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.60
Disease context
Early onset and severe retinal dystrophy with neurological impairment and facial dysmorphia
Similar variants
- GPATCH11 c.328+1G>T Pathogenic same condition
- GPATCH11 p.Arg152Ter Pathogenic same condition
- GPATCH11 p.Tyr131Ter Pathogenic same condition
- GPATCH11 p.Ala146Ser Uncertain significance ★ ⚠ same type
- GPATCH11 p.Ala36Val Uncertain significance ★ ⚠ same type
- GPATCH11 p.Ala46Val Uncertain significance ★ ⚠ same type
- GPATCH11 p.Arg152Gln Uncertain significance ★ ⚠ same type
- GPATCH11 p.Asn75Lys Uncertain significance ★ ⚠ 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/gpatch11-c-449-plus-1g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown