MAP1A

Chr 15

microtubule associated protein 1A

Also known as: MAP1L, MTAP1A

NCBI Gene: 4130 ENSG00000166963 UniProt: P78559 OMIM: 600178

This gene encodes a protein that belongs to the microtubule-associated protein family. The proteins of this family are thought to be involved in microtubule assembly, which is an essential step in neurogenesis. The product of this gene is a precursor polypeptide that presumably undergoes proteolytic processing to generate the final MAP1A heavy chain and LC2 light chain. Expression of this gene is almost exclusively in the brain. Studies of the rat microtubule-associated protein 1A gene suggested a role in early events of spinal cord development. [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.19

LOEUF· LoF intol.

LOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.19LOEUF

pLI 1.000

Z-score 7.45

OE 0.11 (0.07–0.19)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

2.01Z-score

OE missense 0.85 (0.82–0.90)

1297 obs / 1517.3 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.11 (0.07–0.19)

0≤0.351.4

Missense OE?0.85 (0.82–0.90)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 9 / 81.6Missense obs/exp: 1297 / 1517.3Syn Z: 1.41

Background carrier burden — how many people carry a rare variant somewhere in MAP1A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 17

3,582 rare PASS variants

Rare truncating (LoF)

1 in 590

190 rare PASS variants

Rare synonymous (reference)

1 in 40

1,458 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MAP1A. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 25	1 in 910
South Asian	~43k	1 in 16	1 in 970
Remaining (unassigned)	~30k	1 in 13	1 in 420
European (Finnish)	~27k	1 in 51	1 in 2,100
Admixed American	~22k	1 in 19	1 in 1,100
African / African American	~21k	1 in 16	1 in 2,800
East Asian	~20k	1 in 16	1 in 1,000
Ashkenazi Jewish	~13k	1 in 76	≈ 1 in 6,400
Middle Eastern	~2,884	1 in 15	≈ 1 in 2,500

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 3 coding exons well covered in gnomAD exomes and genomes.? see exons ↓