NSD3 p.Val79=
c.237G>T · rs578144675 · VCV3043083
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.142%, sas)
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 1.4, phastCons 1 |
| Overall | ||
| CADD | 5.755 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.142%
South Asian · 129/91,084 alleles
Filtering AF
0.122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.114%
Overall
0.00861%
139/1,614,218 alleles · rare
exomes 130/1,461,886 · genomes 9/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.142% | 706 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| European (non-Finnish) | 0.000339% | 295,010 |
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.Val79=
- Coding
- c.237G>T
- MANE Select
- NM_023034
- dbSNP
- rs578144675
- Type
- single nucleotide variant
- Location
- chr8:38347935 (GRCh38)
- Gene constraint
- LOEUF 0.176 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.29 · 25 PDB
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.Ser653= 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.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-val79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown