NLGN1 p.Cys778Phe
c.2333G>T · VCV3665117
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. | ||
| REVEL | 0.775 | moderately pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 31.0 | 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
- NLGN1
- Protein
- p.Cys778Phe
- Coding
- c.2333G>T
- MANE Select
- NM_001365925
- Type
- single nucleotide variant
- Location
- chr3:174281104 (GRCh38)
- Gene constraint
- LOEUF 0.291 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.23 · 2 PDB
- Residue 778
- a UniProt-annotated variant site (in auts20; uncertain significance)
Similar variants
- NLGN1 p.Gln675Arg Uncertain significance ★★ same type
- NLGN1 p.Gly810Arg Uncertain significance ★★ same type
- NLGN1 p.Val325Ile Uncertain significance ★★ same type
- NLGN1 p.Arg334= Benign ★★ same type
- NLGN1 p.Ile456= Benign ★★ same type
- NLGN1 p.Ile801= Benign ★★ same type
- NLGN1 p.Lys474= Benign ★★ same type
- NLGN1 p.Val197= Benign ★★ 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/nlgn1-p-cys778phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown