Is NLGN3 p.Ala32= (c.96G>A) pathogenic?

NLGN3 p.Ala32= (c.96G>A) is classified Likely benign in NLGN3 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-10-23). Very rare (popmax 0.00325%, nfe); Associated with Inborn genetic diseases.

What condition is associated with NLGN3 p.Ala32= (c.96G>A)?

NLGN3 p.Ala32= (c.96G>A) is associated with Inborn genetic diseases (ClinVar).

How common is NLGN3 p.Ala32= (c.96G>A) in the general population?

NLGN3 p.Ala32= (c.96G>A) is very rare (popmax 0.00325%, nfe) (gnomAD).

NLGN3 p.Ala32=

c.96G>A · rs774680366 · VCV1767897

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00325%, nfe)

Conditions

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 4.2	GERP 0.74, phastCons 1
Overall
CADD	8.886	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00325% European (non-Finnish) · 29/893,590 alleles

Filtering AF 0.00228% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00197%

Overall 0.00273% 33/1,208,332 alleles · very rare exomes 33/1,094,731 · genomes 0/113,601 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00325%	30,813
East Asian	0.00297%	33,702
Admixed American	0.00218%	45,832
Finnishnot grpmax-eligible	0.00215%	46,580
Remaining individualsnot grpmax-eligible	0.00211%	47,504

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.Ala32=
Coding: c.96G>A
MANE Select: NM_181303
dbSNP: rs774680366
Type: single nucleotide variant
Location: chrX:71147845 (GRCh38)
Structure: AlphaFold pLDDT 76.80 · 1 PDB

Full NLGN3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NLGN3 p.Ala32Thr 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-ala32 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown