DISC1 p.Leu790=
c.2368T>C · rs1572681101 · VCV736905
Likely benign
Single submitter
Classification
Likely benign
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.5 | GERP -5.4 |
| Overall | ||
| CADD | 1.775 | 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
- DISC1
- Protein
- p.Leu790=
- Coding
- c.2368T>C
- MANE Select
- NM_018662
- dbSNP
- rs1572681101
- Type
- single nucleotide variant
- Location
- chr1:232026495 (GRCh38)
- Gene constraint
- LOEUF 0.893 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.74 · 1 PDB
- Residue 790
- the 'interaction with pafah1b1' region; the 'necessary and sufficient for interaction with pcnt and localization at the centrosome' region; the 'interaction with atf4 and atf5' region
Similar variants
- DISC1 p.Cys187Tyr Uncertain significance ★★ ⚠ same type
- DISC1 p.Arg170Cys Benign ★★ same type
- DISC1 p.Arg345Gln Benign ★★ same type
- DISC1 p.Glu751Gln Benign ★★ same type
- DISC1 p.Leu330Phe Benign ★★ ⚠ same type
- DISC1 p.Pro432Leu Likely benign ★★ same type
- DISC1 p.Ala13Thr Uncertain significance ★ ⚠ same type
- DISC1 p.Ala220Val 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/disc1-p-leu790 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown