NSD3 p.Ser653=
c.1959C>T · rs764548951 · VCV3056359
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0157%, nfe)
Conditions
1
NSD3-related disorder
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 3.4 | GERP 0.94, phastCons 1 |
| Overall | ||
| CADD | 13.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0157%
European (non-Finnish) · 185/1,179,932 alleles
Filtering AF
0.0138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0131%
Overall
0.0128%
207/1,613,534 alleles · ultra-rare
exomes 196/1,461,448 · genomes 11/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0157% | 6,378 |
| Admixed American | 0.015% | 6,666 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,923 |
| South Asian | 0.00329% | 30,349 |
| African / African-American | 0.00267% | 37,439 |
| Finnishnot grpmax-eligible | 0.00156% | 63,972 |
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
- NSD3
- Protein
- p.Ser653=
- Coding
- c.1959C>T
- MANE Select
- NM_023034
- dbSNP
- rs764548951
- Type
- single nucleotide variant
- Location
- chr8:38315939 (GRCh38)
- Gene constraint
- LOEUF 0.176 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.29 · 25 PDB
- Residue 653
- the 'disordered' region
Disease context
NSD3-related disorder
Similar variants
- NSD3 p.Glu462= Likely benign same condition
- NSD3 p.Leu1266= Likely benign same condition
- NSD3 p.Pro464= Likely benign same condition
- NSD3 p.Ser754= Likely benign same condition
- NSD3 p.Val1175Ile Likely benign same condition
- NSD3 p.Val438= Likely benign same condition
- NSD3 p.Val79= Likely benign same condition
- NSD3 p.Ala1212= Benign ★★ 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/nsd3-p-ser653 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown