GNPTG p.Ser68=
c.204G>T · rs777517766 · VCV1106714
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00254%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.034 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>A here scores Δ0.45 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -4.9 | GERP -3.4 |
| Overall | ||
| CADD | 0.196 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00254%
European (non-Finnish) · 30/1,180,044 alleles
Filtering AF
0.0018%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00156%
Overall
0.00186%
30/1,614,140 alleles · very rare
exomes 30/1,461,838 · genomes 0/152,302 · joint denominator
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
- GNPTG
- Protein
- p.Ser68=
- Coding
- c.204G>T
- MANE Select
- NM_032520
- dbSNP
- rs777517766
- Type
- single nucleotide variant
- Location
- chr16:1361768 (GRCh38)
- Gene constraint
- LOEUF 1.369 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63
Similar variants
- GNPTG p.Ser68Ter Pathogenic/Likely pathogenic ★★ same residue
- GNPTG p.Ser68Leu Uncertain significance ★★ ⚠ same residue
- GNPTG p.Ser68fs Pathogenic ★ same residue
- GNPTG c.179-1G>A Likely pathogenic ★★ same type
- GNPTG c.233+1G>A Pathogenic/Likely pathogenic ★★ same type
- GNPTG c.234-1G>A Pathogenic/Likely pathogenic ★★ same type
- GNPTG c.234-1G>C Pathogenic ★★ same type
- GNPTG c.318-1G>A Pathogenic ★★ 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/gnptg-p-ser68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown