NSUN3 p.Lys188=
c.564A>G · rs1288044535 · VCV1972267
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, 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 6.2 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 8.895 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/75,046 alleles
Filtering AF
0.000442%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000186%
3/1,613,792 alleles · very rare
exomes 3/1,461,446 · genomes 0/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,523 |
| European (non-Finnish) | 8.48e-05% | 1,179,842 |
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
- NSUN3
- Protein
- p.Lys188=
- Coding
- c.564A>G
- MANE Select
- NM_022072
- dbSNP
- rs1288044535
- Type
- single nucleotide variant
- Location
- chr3:94094237 (GRCh38)
- Gene constraint
- LOEUF 0.795 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.97
- Residue 188
- a UniProt-annotated variant site (in coxpd48)
Similar variants
- NSUN3 p.Arg218Gln Uncertain significance ★★ same type
- NSUN3 p.Arg296Lys Uncertain significance ★★ ⚠ same type
- NSUN3 p.Arg58Ter Uncertain significance ★★ same type
- NSUN3 p.Asp301Asn Uncertain significance ★★ ⚠ same type
- NSUN3 p.Cys91Ser Uncertain significance ★★ ⚠ same type
- NSUN3 p.Gly34Glu Uncertain significance ★★ ⚠ same type
- NSUN3 p.Leu209Phe Uncertain significance ★★ ⚠ same type
- NSUN3 p.Leu242Gln 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/nsun3-p-lys188 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown