MAP1B p.Ser2398fs
c.7191del · VCV3338097
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
periventricular nodular heterotopia 9
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 6 of 7 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP -0.27, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- MAP1B
- Protein
- p.Ser2398fs
- Coding
- c.7191del
- MANE Select
- NM_005909
- Type
- Deletion
- Location
- chr5:72203739 (GRCh38)
- Gene constraint
- LOEUF 0.105 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.18
- Residue 2398
- a UniProt-annotated variant site (in pvnh9); a UniProt-annotated variant site (in pvnh9; no effect on protein expression); the 'mediates interaction with tmem185a' region
Similar variants
- MAP1B p.Lys781_Ile782insTer Pathogenic ★★ same condition
- MAP1B p.Arg990fs Likely pathogenic ★ same condition
- MAP1B p.Asp1992fs Likely pathogenic ★ same condition
- MAP1B p.Asp2238_Leu2239insTer Likely pathogenic ★ same condition
- MAP1B p.Glu334fs Likely pathogenic ★ same condition
- MAP1B p.Lys2321fs Likely pathogenic ★ same condition
- MAP1B p.Phe294fs Pathogenic ★ same condition
- MAP1B p.Thr2245fs 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/map1b-p-ser2398fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown