Is MAP1A p.Met1829fs (c.5484_5485del) pathogenic?

MAP1A p.Met1829fs (c.54845485del) is classified Pathogenic in MAP1A (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-04). No gnomAD frequency available for this variant; Associated with neurodevelopmental disorder.

What condition is associated with MAP1A p.Met1829fs (c.5484_5485del)?

MAP1A p.Met1829fs (c.5484_5485del) is associated with neurodevelopmental disorder (ClinVar).

How common is MAP1A p.Met1829fs (c.5484_5485del) in the general population?

MAP1A p.Met1829fs (c.5484_5485del) is no gnomAD frequency available for this variant (gnomAD).

MAP1A p.Met1829fs

c.5484_5485del · rs2140209334 · VCV1685937

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurodevelopmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.5	GERP -0.57, phastCons 0.99

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MAP1A
Protein: p.Met1829fs
Coding: c.5484_5485del
MANE Select: NM_002373
dbSNP: rs2140209334
Type: Microsatellite
Location: chr15:43526953 (GRCh38)
Structure: AlphaFold pLDDT 94.44 · 41 PDB

Full MAP1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MAP1A p.Met1829Thr Uncertain significance ★ ⚠ same residue

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/map1a-p-met1829fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown