NSD1 p.Arg526=
c.1578G>A · rs1562205567 · VCV587924
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
1
Inborn genetic diseases
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 3.9 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 7.808 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,080 alleles
Overall
6.2e-05%
1/1,614,052 alleles · very rare
exomes 1/1,461,846 · genomes 0/152,206 · 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.Arg526=
- Coding
- c.1578G>A
- MANE Select
- NM_022455
- dbSNP
- rs1562205567
- Type
- single nucleotide variant
- Location
- chr5:177209977 (GRCh38)
- Gene constraint
- LOEUF 0.144 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 45.26 · 4 PDB
Similar variants
- NSD1 c.5622+1G>A Pathogenic/Likely pathogenic ★★ same condition
- NSD1 p.Trp1709Ter Pathogenic ★★ same condition
- NSD1 p.Ala1850Val Uncertain significance ★★ ⚠ same condition
- NSD1 p.Ala2300Val Uncertain significance ★★ ⚠ same condition
- NSD1 p.Ala2630Asp Uncertain significance ★★ ⚠ same condition
- NSD1 p.Arg106Lys Uncertain significance ★★ ⚠ same condition
- NSD1 p.Arg1587His Uncertain significance ★★ ⚠ same condition
- NSD1 p.Arg218Ile Uncertain significance ★★ ⚠ same condition
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-arg526 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown