NTF4 p.Pro151=
c.453G>A · rs374345134 · VCV3043136
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0834%, sas)
Conditions
1
NTF4-related disorder
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 -6.1 | |
| Overall | ||
| CADD | 0.323 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0834%
South Asian · 76/91,084 alleles
Filtering AF
0.0683%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0628%
Overall
0.00874%
141/1,614,170 alleles · ultra-rare
exomes 129/1,461,834 · genomes 12/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0834% | 1,198 |
| East Asian | 0.0423% | 2,362 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,465 |
| African / African-American | 0.012% | 8,340 |
| European (non-Finnish) | 0.00178% | 56,192 |
| Admixed American | 0.00167% | 60,030 |
| Finnishnot grpmax-eligible | 0.00156% | 63,992 |
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
- NTF4
- Protein
- p.Pro151=
- Coding
- c.453G>A
- MANE Select
- NM_006179
- dbSNP
- rs374345134
- Type
- single nucleotide variant
- Location
- chr19:49061545 (GRCh38)
- Gene constraint
- LOEUF 1.493 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 78.69 · 3 PDB
Disease context
NTF4-related disorder
Similar variants
- NTF4 c.-12-152C>T Likely benign ★★ same type
- NTF4 c.*110A>G Benign ★★ same type
- NTF4 p.Ala88Val Likely benign ★★ same type
- NTF4 p.Arg68Gln Benign ★★ same type
- NTF4 p.Gln174Arg Likely pathogenic ★ same type
- NTF4 p.Ala127Ser Uncertain significance ★ ⚠ same type
- NTF4 p.Ala172Thr Uncertain significance ★ ⚠ same type
- NTF4 p.Ala54Thr 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/ntf4-p-pro151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown