LMAN1L

Chr 15

lectin, mannose binding 1 like

Also known as: ERGIC-53L, ERGL

NCBI Gene: 79748 ENSG00000140506 UniProt: Q9HAT1

This gene encodes a mannose-binding type 1 transmembrane protein that contains an N-terminal lectin-like carbohydrate recognition domain. The encoded protein is similar in structure to lectins found in leguminous plants. This lectin is thought to transport newly synthesized glycoproteins from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment. [provided by RefSeq, Jan 2017]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.19

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.19LOEUF

pLI 0.000

Z-score 0.81

OE 0.83 (0.59–1.19)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.97Z-score

OE missense 0.84 (0.76–0.94)

259 obs / 306.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.83 (0.59–1.19)

0≤0.351.4

Missense OE?0.84 (0.76–0.94)

0≤0.61.4

Synonymous OE?0.92

0≤1.21.6

LoF obs/exp: 22 / 26.5Missense obs/exp: 259 / 306.9Syn Z: 0.67

Background carrier burden — how many people carry a rare variant somewhere in LMAN1L?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 76

687 rare PASS variants

Rare truncating (LoF)

1 in 540

155 rare PASS variants

Rare synonymous (reference)

1 in 140

305 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for LMAN1L. 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 130	1 in 620
South Asian	~43k	1 in 56	1 in 440
Remaining (unassigned)	~30k	1 in 91	1 in 570
European (Finnish)	~27k	1 in 400	1 in 250
Admixed American	~22k	1 in 85	1 in 470
African / African American	~21k	1 in 69	1 in 370
East Asian	~20k	1 in 66	1 in 610
Ashkenazi Jewish	~13k	1 in 210	1 in 910
Middle Eastern	~2,884	1 in 92	1 in 360

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 14 coding exons well covered in gnomAD exomes and genomes.? see exons ↓