NTNG2 p.Ser239=
c.717C>T · rs566856061 · VCV729325
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.831%, sas)
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 -0.58 | GERP -5.6, phastCons 0.021 |
| Overall | ||
| CADD | 13.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.831%
South Asian · 756/90,920 alleles
Filtering AF
0.782%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.763%
Overall
0.0536%
863/1,610,462 alleles · rare
exomes 820/1,458,090 · genomes 43/152,372 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.831% | 120 |
| Middle Eastern | 0.182% | 550 |
| Remaining individualsnot grpmax-eligible | 0.0721% | 1,386 |
| Admixed American | 0.00501% | 19,975 |
| European (non-Finnish) | 0.00399% | 25,063 |
| East Asian | 0.00223% | 44,852 |
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
- NTNG2
- Protein
- p.Ser239=
- Coding
- c.717C>T
- MANE Select
- NM_032536
- dbSNP
- rs566856061
- Type
- single nucleotide variant
- Location
- chr9:132198469 (GRCh38)
- Gene constraint
- LOEUF 0.501 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 85.03 · 3 PDB
- Residue 239
- the laminin n-terminal domain; an α-helix
Similar variants
- NTNG2 p.Arg183Gly Uncertain significance ★★ ⚠ same type
- NTNG2 p.Gly317Ser Uncertain significance ★★ ⚠ same type
- NTNG1 c.1087+10829A>G Benign ★★ same type
- NTNG1 c.1087+10866G>A Benign ★★ same type
- NTNG1 c.887+97C>T Benign ★★ same type
- NTNG1 c.-120G>C Benign ★★ same type
- NTNG1 c.-293A>G Benign ★★ same type
- NTNG1 c.*127A>C Benign ★★ same type
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/ntng2-p-ser239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown