LMCD1 LIM and cysteine rich domains 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LMCD1provided by HGNC
Official Full Name: LIM and cysteine rich domains 1provided by HGNC
Primary source: HGNC:HGNC:6633
See related: Ensembl:ENSG00000071282 MIM:604859; AllianceGenome:HGNC:6633
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: This gene encodes a member of the LIM-domain family of zinc finger proteins. The encoded protein contains an N-terminal cysteine-rich domain and two C-terminal LIM domains. The presence of LIM domains suggests involvement in protein-protein interactions. The protein may act as a co-regulator of transcription along with other transcription factors. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]
Expression: Broad expression in lung (RPKM 21.9), fat (RPKM 21.1) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p25.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (8501823..8574668)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (8492967..8566009)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (8543509..8616354)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

LIM and Cysteine-Rich Domains 1 Promotes Transforming Growth Factor beta1-Induced Epithelial-Mesenchymal Transition in Human Kidney 2 Cells.
Title: LIM and Cysteine-Rich Domains 1 Promotes Transforming Growth Factor β1-Induced Epithelial-Mesenchymal Transition in Human Kidney 2 Cells.
Critical Role of LMCD1 in Promoting Profibrotic Characteristics of Lung Myofibroblasts in Experimental and Scleroderma-Associated Lung Fibrosis.
Title: Critical Role of LMCD1 in Promoting Profibrotic Characteristics of Lung Myofibroblasts in Experimental and Scleroderma-Associated Lung Fibrosis.
LMCD1 facilitates the induction of pluripotency via cell proliferation, metabolism, and epithelial-mesenchymal transition.
Title: LMCD1 facilitates the induction of pluripotency via cell proliferation, metabolism, and epithelial-mesenchymal transition.
LMCD1 promotes osteogenic differentiation of human bone marrow stem cells by regulating BMP signaling.
Title: LMCD1 promotes osteogenic differentiation of human bone marrow stem cells by regulating BMP signaling.
LMCD1 acts as an activator of E2F1 in humans in the induction of CDC6 and IL-33 expression during development of vascular lesions.
Title: Myristoylation of LMCD1 Leads to Its Species-Specific Derepression of E2F1 and NFATc1 in the Modulation of CDC6 and IL-33 Expression During Development of Vascular Lesions.
Skeletal muscle LMCD1 expression is reduced in patients with skeletal muscle disease. We analyzed gene expression data from muscle of patients with diverse muscle pathologies and identified LMCD1 as a gene strongly associated with skeletal muscle function.
Title: LIM and cysteine-rich domains 1 (LMCD1) regulates skeletal muscle hypertrophy, calcium handling, and force.
LIM and cysteine-rich domains 1 is required for thrombin-induced smooth muscle cell proliferation and promotes atherogenesis
Title: LIM and cysteine-rich domains 1 is required for thrombin-induced smooth muscle cell proliferation and promotes atherogenesis.
The rs1800775 [1.31 (1.22-1.42); p = 3.41E-12] in the CETP gene and rs359027 [1.26 (1.16-1.36); p = 2.55E-08] in the LMCD1 gene were significantly associated with LHDLC levels
Title: A common variant association study reveals novel susceptibility loci for low HDL-cholesterol levels in ethnic Arabs.
Together, our results suggest that LMCD1 mutations are potential oncogenic events in HCC metastasis to promote cell migration through the Rac1-signaling pathway.
Title: Somatic LMCD1 mutations promoted cell migration and tumor metastasis in hepatocellular carcinoma.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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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-76678 (e-PCR)
- UniSTS:58183

RH78679 (e-PCR)
- UniSTS:22894

STS-N95054 (e-PCR)
- UniSTS:10358

RH118390 (e-PCR)
- UniSTS:209626

RH93928 (e-PCR)
- UniSTS:89326

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription corepressor activity	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of calcineurin-NFAT signaling cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cardiac muscle hypertrophy	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: LIM and cysteine-rich domains protein 1

Names: dyxin

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_001278233.2 → NP_001265162.1 LIM and cysteine-rich domains protein 1 isoform 2

See identical proteins and their annotated locations for NP_001265162.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region and uses a downstream start codon compared to variant 1. The encoded isoform (2) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

AC087859, AK294455, BC000646, BU619403, CN388104

Consensus CDS

CCDS63534.1

UniProtKB/Swiss-Prot

Q9NZU5

Related

ENSP00000396515.1, ENST00000454244.4

Conserved Domains (3) summary

cd09340
Location:170 → 227

LIM1_Testin_like; The first LIM domain of Testin-like family

cd09829
Location:43 → 130

PET_testin; The PET domain of Testin

cl02475
Location:233 → 286

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
NM_001278234.2 → NP_001265163.1 LIM and cysteine-rich domains protein 1 isoform 3

See identical proteins and their annotated locations for NP_001265163.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate exon and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AC087859, AK293849, BC000646, BU619403, CN388104

Consensus CDS

CCDS63533.1

UniProtKB/TrEMBL

B4DEY6

Related

ENSP00000380542.3, ENST00000397386.7

Conserved Domains (3) summary

cd09340
Location:131 → 188

LIM1_Testin_like; The first LIM domain of Testin-like family

cd09829
Location:18 → 91

PET_testin; The PET domain of Testin

cl02475
Location:194 → 247

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
NM_001278235.2 → NP_001265164.1 LIM and cysteine-rich domains protein 1 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate 3' terminal exon which results in an early stop codon, compared to variant 1. It encodes isoform 4, which has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AI693011, AI951010, AK300803, BC000646, BX114807, N95437, W47274

Consensus CDS

CCDS63532.1

UniProtKB/TrEMBL

B7Z6R5, H7C3D2

Related

ENSP00000411222.2, ENST00000426878.2

Conserved Domains (1) summary

cd09829
Location:116 → 203

PET_testin; The PET domain of Testin
NM_014583.4 → NP_055398.1 LIM and cysteine-rich domains protein 1 isoform 1

See identical proteins and their annotated locations for NP_055398.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC087859, AF169284, BU619403, CN388104

Consensus CDS

CCDS33688.1

UniProtKB/Swiss-Prot

B4DG80, Q9NZU5

Related

ENSP00000157600.3, ENST00000157600.8

Conserved Domains (3) summary

cd09340
Location:243 → 300

LIM1_Testin_like; The first LIM domain of Testin-like family

cd09829
Location:116 → 203

PET_testin; The PET domain of Testin

cl02475
Location:306 → 359

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers