NRXN1 p.Arg900=
c.2698A>C · rs574531814 · VCV336548
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0668%, eas)
Conditions
2
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 5.3 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 12.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0668%
East Asian · 30/44,878 alleles
Filtering AF
0.0481%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0417%
Overall
0.0026%
42/1,613,950 alleles · ultra-rare
exomes 38/1,461,636 · genomes 4/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0668% | 1,496 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,413 |
| South Asian | 0.00659% | 15,180 |
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
- NRXN1
- Protein
- p.Arg900=
- Coding
- c.2698A>C
- MANE Select
- NM_001330078
- dbSNP
- rs574531814
- Type
- single nucleotide variant
- Location
- chr2:50497514 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.53 · 3 PDB
Similar variants
- NRXN1 p.Arg900Gly Uncertain significance ★ ⚠ same residue
- NRXN1 c.832+1G>A Likely pathogenic ★★ same condition
- NRXN1 p.Arg1144Ter Pathogenic/Likely pathogenic ★★ same condition
- NRXN1 p.Arg1253Ter Pathogenic/Likely pathogenic ★★ same condition
- NRXN1 p.Arg1260Ter Pathogenic ★★ same condition
- NRXN1 p.Arg747Ter Likely pathogenic ★★ same condition
- NRXN1 p.Arg855Ter Pathogenic/Likely pathogenic ★★ same condition
- NRXN1 c.1320+3A>G Uncertain significance ★★ 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/nrxn1-p-arg900 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown