NLGN3 p.Pro16=
c.48C>T · rs745903511 · VCV1743952
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0437%, afr)
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 3.1 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 7.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0437%
African / African-American · 25/57,232 alleles
Filtering AF
0.0304%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0259%
Overall
0.00265%
32/1,208,576 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0437% | 2,289 |
| Remaining individualsnot grpmax-eligible | 0.0126% | 7,922 |
| European (non-Finnish) | 0.000112% | 894,678 |
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.Pro16=
- Coding
- c.48C>T
- MANE Select
- NM_181303
- dbSNP
- rs745903511
- Type
- single nucleotide variant
- Location
- chrX:71147797 (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-pro16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown