LRRTM1 leucine rich repeat transmembrane neuronal 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LRRTM1provided by HGNC
Official Full Name: leucine rich repeat transmembrane neuronal 1provided by HGNC
Primary source: HGNC:HGNC:19408
See related: Ensembl:ENSG00000162951 MIM:610867; AllianceGenome:HGNC:19408
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Predicted to be involved in regulation of postsynaptic density assembly and regulation of presynapse assembly. Predicted to act upstream of or within several processes, including long-term synaptic potentiation; negative regulation of receptor internalization; and positive regulation of synapse assembly. Located in endoplasmic reticulum and growth cone. Is active in GABA-ergic synapse and postsynaptic specialization membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in brain (RPKM 4.5), salivary gland (RPKM 2.3) and 7 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p12

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (80288356..80304752, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (80302025..80304899, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (80529003..80531877, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Functional cerebral asymmetries in the language domain are associated with the rs6733871 LRRTM1 polymorphism during cognitive control and top-down attention mechanisms.
Title: Cognitive Control Processes and Functional Cerebral Asymmetries: Association with Variation in the Handedness-Associated Gene LRRTM1.
Continuity between schizophrenia and schizotypy exists with regard to the psychological effects of allelic variation in LRRTM1, and epigenetic variation in the imprinted gene mediates the development and expression of human handedness.
Title: The imprinted gene LRRTM1 mediates schizotypy and handedness in a nonclinical population.
Hypomethylation of the paternally inherited LRRTM1 promoter is linked to schizophrenia.
Title: Hypomethylation of the paternally inherited LRRTM1 promoter linked to schizophrenia.
CTNNA1 and CTNNA2 contain alternative 5' exons linked to bidirectional promoters that are shared with the antisense oriented LRRTM2 and LRRTM1 genes, respectively.
Title: Bidirectional transcription from human LRRTM2/CTNNA1 and LRRTM1/CTNNA2 gene loci leads to expression of N-terminally truncated CTNNA1 and CTNNA2 isoforms.
16 SNPs in 12 genes showed significant interaction at P < .05, 3 of which survived correction for multiple testing (P < .0003), situated in AKT1 (rs2494732 and rs1130233) and LRRTM1 (rs673871).
Title: Family-based analysis of genetic variation underlying psychosis-inducing effects of cannabis: sibling analysis and proband follow-up.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Family-based analysis of genetic variation underlying psychosis-inducing effects of cannabis: sibling analysis and proband follow-up.
Observational study of gene-disease association. (HuGE Navigator)
Title: Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry.
Results strengthen the evidence for an association of imprinted alleles of LRRTM1 with schizophrenia. Weaker supportive evidence was also obtained for a possible association of LRTTM1 with human brain asymmetry.
Title: Supporting evidence for LRRTM1 imprinting effects in schizophrenia.
Recent study in which the first putative genetic effect on human handedness was identified (the imprinted locus LRRTM1 on human chromosome 2).
Title: Understanding the genetics of behavioural and psychiatric traits will only be achieved through a realistic assessment of their complexity.
While we agree (and indeed first proposed) that the variation underlying psychosis is intrinsically related to the cerebral torque, which we take to be the anatomical basis of language, we are unconvinced by the data for LRRTM1.
Title: Where and what is the right shift factor or cerebral dominance gene? A critique of Francks et al. (2007).

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-79114 (e-PCR)
- UniSTS:95811

LRRTM1__7335 (e-PCR)
- UniSTS:466282

D2S1942E (e-PCR)
- UniSTS:153725

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
involved_in exploration behavior	IEA Inferred from Electronic Annotation more info
involved_in locomotory behavior	IEA Inferred from Electronic Annotation more info
involved_in long-term synaptic potentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of receptor internalization	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of synapse assembly	IEA Inferred from Electronic Annotation more info
involved_in protein localization to synapse	IEA Inferred from Electronic Annotation more info
involved_in receptor internalization	IEA Inferred from Electronic Annotation more info
involved_in regulation of postsynaptic density assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of presynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in synapse organization	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in GABA-ergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in axon	IDA Inferred from Direct Assay more info	PubMed
NOT located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in excitatory synapse	IEA Inferred from Electronic Annotation more info
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in growth cone	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic specialization membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic specialization membrane	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: leucine-rich repeat transmembrane neuronal protein 1

Names: leucine-rich repeat transmembrane neuronal 1 protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_178839.5 → NP_849161.2 leucine-rich repeat transmembrane neuronal protein 1 precursor

See identical proteins and their annotated locations for NP_849161.2

Status: VALIDATED

Source sequence(s)

AA977181, AC016670, AY182024, BI756350

Consensus CDS

CCDS1966.1

UniProtKB/Swiss-Prot

A8K397, D6W5K1, Q86UE6, Q96DN1

Related

ENSP00000295057.3, ENST00000295057.4

Conserved Domains (5) summary

cd00116
Location:85 → 268

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00031
Location:306 → 318

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:91 → 114

LRR_RI; leucine-rich repeat [structural motif]

pfam12799
Location:257 → 297

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:113 → 173

LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

80288356..80304752 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047444146.1 → XP_047300102.1 leucine-rich repeat transmembrane neuronal protein 1 isoform X1

UniProtKB/Swiss-Prot

A8K397, D6W5K1, Q86UE6, Q96DN1

Related

ENSP00000393562.1, ENST00000417012.5
XM_017003987.3 → XP_016859476.1 leucine-rich repeat transmembrane neuronal protein 1 isoform X1

UniProtKB/Swiss-Prot

A8K397, D6W5K1, Q86UE6, Q96DN1

Conserved Domains (5) summary

cd00116
Location:85 → 268

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00031
Location:306 → 318

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:91 → 114

LRR_RI; leucine-rich repeat [structural motif]

pfam12799
Location:257 → 297

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:113 → 173

LRR_8; Leucine rich repeat
XM_017003986.3 → XP_016859475.1 leucine-rich repeat transmembrane neuronal protein 1 isoform X1

UniProtKB/Swiss-Prot

A8K397, D6W5K1, Q86UE6, Q96DN1

Conserved Domains (5) summary

cd00116
Location:85 → 268

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00031
Location:306 → 318

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:91 → 114

LRR_RI; leucine-rich repeat [structural motif]

pfam12799
Location:257 → 297

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:113 → 173

LRR_8; Leucine rich repeat

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

80302025..80304899 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054341769.1 → XP_054197744.1 leucine-rich repeat transmembrane neuronal protein 1 isoform X1

UniProtKB/Swiss-Prot

A8K397, D6W5K1, Q86UE6, Q96DN1
XM_054341768.1 → XP_054197743.1 leucine-rich repeat transmembrane neuronal protein 1 isoform X1

UniProtKB/Swiss-Prot

A8K397, D6W5K1, Q86UE6, Q96DN1