MAP1B p.Ser1247Ter
c.3740C>A · rs1310873497 · VCV3254681
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
periventricular nodular heterotopia 9
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 7 |
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP 0.58, phastCons 0.041 |
| Overall | ||
| CADD | 31.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- MAP1B
- Protein
- p.Ser1247Ter
- Coding
- c.3740C>A
- MANE Select
- NM_005909
- dbSNP
- rs1310873497
- Type
- single nucleotide variant
- Location
- chr5:72197095 (GRCh38)
- Gene constraint
- LOEUF 0.105 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.18
- Residue 1247
- a UniProt-annotated variant site (in pvnh9); a UniProt-annotated variant site (in pvnh9; no effect on protein expression); the 'disordered' region; a modified residue (phosphoserine)
Similar variants
- MAP1B p.Arg1664Ter Pathogenic/Likely pathogenic ★★ same condition
- MAP1B p.Arg303Ter Pathogenic/Likely pathogenic ★★ same condition
- MAP1B p.Arg85Ter Pathogenic/Likely pathogenic ★★ same condition
- MAP1B p.Arg999Ter Pathogenic/Likely pathogenic ★★ same condition
- MAP1B p.Arg1399Cys Uncertain significance ★★ ⚠ same condition
- MAP1B p.Glu1944Lys Uncertain significance ★★ ⚠ same condition
- MAP1B p.Leu1453Val Uncertain significance ★★ ⚠ same condition
- MAP1B p.Lys2253Arg Uncertain significance ★★ ⚠ 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-ser1247ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown