NSD1 p.Pro231=
c.693T>A · VCV3642142
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, 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 6 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 11.26 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
African / African-American · 11/74,834 alleles
Filtering AF
0.00816%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00634%
Overall
0.000683%
11/1,611,652 alleles · ultra-rare
exomes 4/1,459,502 · genomes 7/152,150 · 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
- NSD1
- Protein
- p.Pro231=
- Coding
- c.693T>A
- MANE Select
- NM_022455
- Type
- single nucleotide variant
- Location
- chr5:177135796 (GRCh38)
- Gene constraint
- LOEUF 0.144 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 45.26 · 4 PDB
- Residue 231
- the 'disordered' region
Similar variants
- NSD1 p.Pro231Leu Uncertain significance ★ ⚠ same residue
- NSD1 p.Pro231Ser Likely benign ★ same residue
- NSD1 c.1064-2A>G Pathogenic/Likely pathogenic ★★ same type
- NSD1 c.3921+1G>A Likely pathogenic ★★ same type
- NSD1 c.4192+2T>G Pathogenic ★★ same type
- NSD1 c.4303-1G>C Likely pathogenic ★★ same type
- NSD1 c.4378+1G>A Pathogenic/Likely pathogenic ★★ same type
- NSD1 c.4766-2A>G Pathogenic/Likely 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/nsd1-p-pro231 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown