NLGN3 p.Val232=
c.696C>T · rs1210930898 · VCV1753105
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000447%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 8.761 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000447%
European (non-Finnish) · 4/895,600 alleles
Filtering AF
0.000105%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.1e-05%
Overall
0.00033%
4/1,212,355 alleles · very rare
exomes 4/1,098,165 · genomes 0/114,190 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NLGN3
- Protein
- p.Val232=
- Coding
- c.696C>T
- MANE Select
- NM_181303
- dbSNP
- rs1210930898
- Type
- single nucleotide variant
- Location
- chrX:71155332 (GRCh38)
- Structure
- AlphaFold pLDDT 76.80 · 1 PDB
Similar variants
- NLGN3 p.Val232Ile Uncertain significance ★ ⚠ same residue
- NLGN3 p.Arg785Cys Uncertain significance ★★ ⚠ same condition
- NLGN3 p.Leu31Phe Uncertain significance ★★ ⚠ same condition
- NLGN3 p.Leu477Phe Uncertain significance ★★ ⚠ same condition
- NLGN3 p.Thr783Met Uncertain significance ★★ ⚠ same condition
- NLGN3 p.Val346Met Uncertain significance ★★ ⚠ same condition
- NLGN3 p.Ala750= Benign ★★ same condition
- NLGN3 p.Asn138= Likely benign ★★ 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/nlgn3-p-val232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown