NTNG2 p.Ser205=
c.615C>G · rs368226145 · VCV2659643
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0186%, nfe)
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 4 | GERP 0.64, phastCons 1 |
| Overall | ||
| CADD | 12.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0186%
European (non-Finnish) · 220/1,179,966 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0158%
Overall
0.0145%
234/1,612,864 alleles · ultra-rare
exomes 220/1,460,606 · genomes 14/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0186% | 5,363 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,808 |
| Admixed American | 0.00833% | 11,999 |
| African / African-American | 0.00133% | 74,944 |
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.Ser205=
- Coding
- c.615C>G
- MANE Select
- NM_032536
- dbSNP
- rs368226145
- Type
- single nucleotide variant
- Location
- chr9:132198367 (GRCh38)
- Gene constraint
- LOEUF 0.501 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 85.03 · 3 PDB
- Residue 205
- the laminin n-terminal domain; a β-strand
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-ser205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown