NLGN3 p.Pro790=
c.2370C>T · rs372131545 · VCV725262
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.107%, amr)
Conditions
1
Inborn genetic diseases
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 -5.5 | GERP -3.8 |
| Overall | ||
| CADD | 0.319 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.107%
Admixed American · 48/44,661 alleles
Filtering AF
0.0833%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0747%
Overall
0.00517%
62/1,199,648 alleles · rare
exomes 57/1,088,923 · genomes 5/110,725 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.107% | 930 |
| South Asian | 0.0144% | 6,928 |
| Remaining individualsnot grpmax-eligible | 0.00423% | 23,625 |
| African / African-American | 0.00177% | 56,540 |
| European (non-Finnish) | 0.000337% | 296,731 |
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.Pro790=
- Coding
- c.2370C>T
- MANE Select
- NM_181303
- dbSNP
- rs372131545
- Type
- single nucleotide variant
- Location
- chrX:71169920 (GRCh38)
- Structure
- AlphaFold pLDDT 76.80 · 1 PDB
Similar variants
- 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
- NLGN3 p.Asn138Ser 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-pro790 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown