NSUN2 p.Val164fs
c.491_510del · VCV4969390
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
NSUN2-related disorders
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 19 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.45 | GERP -4.6, phastCons 0.92 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NSUN2
- Protein
- p.Val164fs
- Coding
- c.491_510del
- MANE Select
- NM_017755
- Type
- Deletion
- Location
- chr5:6623241 (GRCh38)
- Gene constraint
- LOEUF 0.965 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.09 · 11 PDB
Disease context
NSUN2-related disorders
Similar variants
- NSUN2 c.1600_1601+2del Likely pathogenic ★ same condition
- NSUN2 p.Ser432Ter Likely pathogenic ★ same condition
- NSUN2 p.Asn493fs Pathogenic ★★ same type
- NSUN2 p.Gly341fs Pathogenic ★★ same type
- NSUN2 p.Ser575fs Pathogenic/Likely pathogenic ★★ same type
- NSUN2 c.1021+16_1021+19del Benign/Likely benign ★★ same type
- NSUN2 c.1602-17_1602-15del Benign/Likely benign ★★ same type
- NSUN2 c.466-8del Benign/Likely 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/nsun2-p-val164fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown