COLQ p.Asp392=
c.1176T>C · rs794727145 · VCV194521
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.85 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.5 | GERP -4.3 |
| Overall | ||
| CADD | 0.9 | PHRED · no single calibrated threshold — expert panels disagree |
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
- COLQ
- Protein
- p.Asp392=
- Coding
- c.1176T>C
- MANE Select
- NM_005677
- dbSNP
- rs794727145
- Type
- single nucleotide variant
- Location
- chr3:15455918 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 55.25 · 2 PDB
- Residue 392
- a UniProt-annotated variant site (in cms5; pathogenic); a UniProt-annotated variant site (in cms5; pathogenic; impaired anchoring of asymmetric ache to the synaptic basal membrane); a UniProt-annotated variant site (in cms5; likely pathogenic; impaired anchoring of asymmetric ache to the synaptic basal membrane)
Similar variants
- COLQ p.Asp392Asn Uncertain significance ★★ ⚠ same residue
- COLQ c.1195+1G>A Pathogenic ★★ same type
- COLQ c.1298+3A>G Pathogenic ★★ same type
- COLQ c.219+1G>C Pathogenic ★★ same type
- COLQ c.220-1G>A Pathogenic/Likely pathogenic ★★ same type
- COLQ c.393+1G>A Pathogenic ★★ same type
- COLQ c.529-2A>G Pathogenic/Likely pathogenic ★★ same type
- COLQ c.555+1G>A 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/colq-p-asp392 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown