ASNS p.Val199fs
c.594del · VCV3594972
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
congenital microcephaly - severe encephalopathy - progressive cerebral atrophy syndrome
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 13 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP 0.87, phastCons 1 |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ASNS
- Protein
- p.Val199fs
- Coding
- c.594del
- MANE Select
- NM_001673
- Type
- Deletion
- Location
- chr7:97859292 (GRCh38)
- Gene constraint
- LOEUF 0.745 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.36 · 3 PDB
- Residue 199
- a β-strand
Disease context
congenital microcephaly - severe encephalopathy - progressive cerebral atrophy syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Congenital microcephaly-severe encephalopathy-progressive cerebral atrophy syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- ASNS c.1137+200_1137+205del Likely pathogenic ★★ same condition
- ASNS c.1239-1del Likely pathogenic ★★ same condition
- ASNS c.904-3_904-1del Likely pathogenic ★★ same condition
- ASNS p.Arg236fs Pathogenic/Likely pathogenic ★★ same condition
- ASNS p.Asn456fs Pathogenic/Likely pathogenic ★★ same condition
- ASNS p.Glu160fs Pathogenic/Likely pathogenic ★★ same condition
- ASNS p.Leu181fs Pathogenic/Likely pathogenic ★★ same condition
- ASNS p.Lys354fs Pathogenic/Likely pathogenic ★★ 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/asns-p-val199fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown