LYSMD2

Chr 15

LysM domain containing 2

NCBI Gene: 256586 ENSG00000140280 UniProt: Q8IV50

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

0.91

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.91LOEUF

pLI 0.416

Z-score 1.71

OE 0.19 (0.07–0.91)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.21Z-score

OE missense 0.93 (0.77–1.14)

70 obs / 75.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.19 (0.07–0.91)

0≤0.351.4

Missense OE?0.93 (0.77–1.14)

0≤0.61.4

Synonymous OE?0.71

0≤1.21.6

LoF obs/exp: 1 / 5.2Missense obs/exp: 70 / 75.1Syn Z: 1.26

Background carrier burden — how many people carry a rare variant somewhere in LYSMD2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 140

293 rare PASS variants

Rare truncating (LoF)

1 in 500

40 rare PASS variants

Rare synonymous (reference)

1 in 750

120 rare PASS variants

Rare missense and truncating variants are carried at similar rates in LYSMD2; this gene does not show strong loss-of-function constraint by this measure. 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 490	1 in 3,200
South Asian	~43k	1 in 180	1 in 3,400
Remaining (unassigned)	~30k	1 in 170	1 in 1,100
European (Finnish)	~27k	1 in 640	≈ 1 in 6,500
Admixed American	~22k	1 in 130	≈ 1 in 5,600
African / African American	~21k	1 in 230	≈ 1 in 21,000
East Asian	~20k	1 in 360	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 540	≈ 1 in 6,600
Middle Eastern	~2,884	1 in 330	none seen

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): 2 of 3 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 3.? see exons ↓