LRTM1

protein-coding

leucine rich repeats and transmembrane domains 1

Gene summary

Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020678.4

Inheritance

—

ClinVar variants

U:47B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.46

Max pathogenic AF

—

Genomic locus

chr3:54,918,231-54,967,088

External References & Databases

Ensembl (ENSG00000144771)

Transcript & Mutation Effects

hg38 • Region Span ~48.9 kb

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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 LRTM1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 52

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020678.4. 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				1 clinvar		1
missense			47 clinvar	4 clinvar	3 clinvar	54
nonsense					1 clinvar	1
start loss						0
frameshift				2 clinvar		2
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	7	4	58

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020678.4	RefSeq	NP_065729.1	3	MANE Select
ENST00000273286.6	Ensembl	ENSP00000273286.5	3	MANE Select
NM_001304389.2	RefSeq	NP_001291318.1	2	Standard
ENST00000493075.1	Ensembl	ENSP00000419772.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of synapse assembly

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273286
Coding exons: 3
Length: 48852
Individuals with no LoFs: 125233
Homozygous LoFs: 2
Heterozygous LoFs: 512
Defined: 125747
p: 0.00205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.837	221	189	1.17	0.00000974	2228
Missense (PolyPhen)		74	63.846	1.159		777
Synonymous	-0.840	92	82.3	1.12	0.00000495	717
Loss of Function	-1.57	20	13.7	1.46	8.02e-7	137

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00067	0.00067	rare
Ashkenazi Jewish	0.011	0.011	notable
East Asian	0.0070	0.0070	notable
Finnish	0.00046	0.00046	rare
European (Non-Finnish)	0.0012	0.0012	notable
South Asian	0.0030	0.0029	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0771

Intolerance Scores

LoFtool: 0.791
RVIS EVS: 0.82
RVIS percentile EVS: 87.99

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0431

Gene Damage Prediction

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