NNT p.Pro47=
c.141T>G · VCV3689924
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.04%, afr)
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 -0.38 | GERP -0.92, phastCons 0.002 |
| Overall | ||
| CADD | 4.356 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.04%
African / African-American · 30/74,914 alleles
Filtering AF
0.0288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0249%
Overall
0.00192%
31/1,613,724 alleles · ultra-rare
exomes 17/1,461,512 · genomes 14/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.04% | 2,497 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
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
- NNT
- Protein
- p.Pro47=
- Coding
- c.141T>G
- MANE Select
- NM_182977
- Type
- single nucleotide variant
- Location
- chr5:43609336 (GRCh38)
- Gene constraint
- LOEUF 0.588 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.80 · 3 PDB
Similar variants
- NNT c.3112-3C>T Uncertain significance ★★ same type
- NNT p.Ala1078Val Uncertain significance ★★ ⚠ same type
- NNT p.Ala661Val Uncertain significance ★★ ⚠ same type
- NNT p.Arg587His Uncertain significance ★★ ⚠ same type
- NNT p.Asp915Gly Uncertain significance ★★ ⚠ same type
- NNT p.Gly282Asp Uncertain significance ★★ ⚠ same type
- NNT p.Ile1024Met Uncertain significance ★★ ⚠ same type
- NNT p.Ile534Val Uncertain significance ★★ ⚠ 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/nnt-p-pro47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown