GNPTG p.Ser152=
c.456C>T · rs760954235 · VCV1098061
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 -8.3 | GERP -3.3 |
| Overall | ||
| CADD | 0.608 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,894 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00134%
Overall
0.00254%
41/1,613,414 alleles · very rare
exomes 35/1,461,164 · genomes 6/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,965 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,617 |
| South Asian | 0.00329% | 30,363 |
| Finnishnot grpmax-eligible | 0.00315% | 31,723 |
| African / African-American | 0.00267% | 37,471 |
| European (non-Finnish) | 0.00229% | 43,702 |
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.Ser152=
- Coding
- c.456C>T
- MANE Select
- NM_032520
- dbSNP
- rs760954235
- Type
- single nucleotide variant
- Location
- chr16:1362250 (GRCh38)
- Gene constraint
- LOEUF 1.369 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63
- Residue 152
- the mrh domain
Similar variants
- 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
- GNPTG c.52+1G>C Likely pathogenic ★★ same type
- GNPTG c.526+2T>G Likely pathogenic ★★ same type
- GNPTG c.610-1G>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-ser152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown