LYSMD3

protein-coding

LysM domain containing 3

Gene summary

Enables peptidoglycan binding activity. Involved in Golgi organization. Located in Golgi membrane and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_198273.2

Inheritance

—

ClinVar variants

U:36B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr5:90,515,611-90,529,584

External References & Databases

Ensembl (ENSG00000176018)

Transcript & Mutation Effects

hg38 • Region Span ~14.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LYSMD3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198273.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			36 clinvar	1 clinvar	1 clinvar	38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	3	1	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198273.2	RefSeq	NP_938014.1	2	MANE Select
ENST00000315948.11	Ensembl	ENSP00000314518.6	2	MANE Select
NM_001286812.1	RefSeq	NP_001273741.1	2	Standard
ENST00000453259.2	Ensembl	ENSP00000405507.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000315948
Coding exons: 2
Length: 13974
Individuals with no LoFs: 124770
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 124783
p: 0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.324	151	163	0.928	0.00000825	2002
Missense (PolyPhen)		40	55.389	0.72216		694
Synonymous	0.805	47	54.6	0.861	0.00000270	575
Loss of Function	2.50	3	12.6	0.239	7.66e-7	146

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.00013	0.00013	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0911

Intolerance Scores

LoFtool: 0.764
RVIS EVS: 0.06
RVIS percentile EVS: 58.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0865

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium