LYSMD1

Chr 1

LysM domain containing 1

Also known as: SB145

NCBI Gene: 388695 ENSG00000163155 UniProt: Q96S90

Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Research

Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

MultiplemechanismLOEUF 1.05

Clinical Summary— LYSMD1

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Population Constraint (gnomAD)

Low constraint (pLI 0.02) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

54 VUS of 65 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.05LOEUF

pLI 0.018

Z-score 1.48

OE 0.46 (0.23–1.05)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.73Z-score

OE missense 0.82 (0.70–0.96)

109 obs / 132.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.46 (0.23–1.05)

0≤0.351.4

Missense OE?0.82 (0.70–0.96)

0≤0.61.4

Synonymous OE?0.92

0≤1.21.6

LoF obs/exp: 4 / 8.7Missense obs/exp: 109 / 132.7Syn Z: 0.46

This gene — mechanism propensity

0.75top 25%

GOF

0.7028th %ile

LOF

0.3067th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

65 submitted variants in ClinVar

ClinVar

Classification Summary

VUS54

Likely Benign1

Benign3

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	1	53	0	54
Likely Benign	0	1	0	1
Benign	0	1	2	3
Total	1	55	2	58

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

15 pathogenic / likely-pathogenic (of 18) ClinVar copy-number / structural variants overlap LYSMD1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →