LMOD2

leiomodin 2, the group of Leiomodins

Basic information

Region (hg38): 7:123655866-123664290

Links

ENSG00000170807 ∙ NCBI:442721 ∙ OMIM:608006 ∙ HGNC:6648 ∙ Uniprot:Q6P5Q4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 3 of 3.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_207163.3	NP_997046.1	3	yes	-
ENST00000458573.3	ENSP00000411932.2	3	yes	-
ENST00000456238.2	ENSP00000398975.2	2	-	-

Phenotypes

GenCC

Source: genCC

• cardiomyopathy, dilated, 2G (Strong), mode of inheritance: AR
• dilated cardiomyopathy (Definitive), mode of inheritance: AR
• cardiomyopathy, dilated, 2G (Strong), mode of inheritance: AR
• cardiomyopathy, dilated, 2G (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cardiomyopathy, dilated, 2G	AR	Cardiovascular	The condition involves severe and early-onset dilated cardiomyopathy (which can be lethal), but awareness can allow early medical and surgical management; Heart transplant has been described	Cardiovascular	31517052; 34888509; 35188328; 35082396

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMOD2 gene.

• Inborn_genetic_diseases (84 variants)
• Cardiomyopathy,_dilated,_2G (8 variants)
• not_provided (2 variants)
• LMOD2-related_condition (2 variants)
• Familial_isolated_dilated_cardiomyopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMOD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_207163.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			83	4		87
nonsense	2					2
start loss						0
frameshift	1	3				4
splice donor/acceptor (+/-2bp)	1					1
Total	4	3	83	4	1

Highest pathogenic variant AF is 0.000007663579

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMOD2	protein_coding	protein_coding	ENST00000458573	3	8484

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124630	0	20	124650	0.0000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.271	282	295	0.956	0.0000158	3584
Missense in Polyphen		117	122.5	0.95507		1448
Synonymous	0.117	115	117	0.986	0.00000695	1055
Loss of Function	2.00	8	16.8	0.475	8.77e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000984	0.0000935
Ashkenazi Jewish	0.000103	0.0000994
East Asian	0.000226	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000115
Middle Eastern	0.000226	0.000223
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates nucleation of actin filaments and thereby promotes actin polymerization (PubMed:18403713, PubMed:26370058, PubMed:25250574, PubMed:26417072). Plays a role in the regulation of actin filament length (By similarity). Required for normal sarcomere organization in the heart, and for normal heart function (PubMed:18403713). {ECO:0000250|UniProtKB:Q3UHZ5, ECO:0000269|PubMed:18403713, ECO:0000269|PubMed:25250574, ECO:0000269|PubMed:26370058, ECO:0000269|PubMed:26417072}.

Intolerance Scores

• loftool: 0.399
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0879

Gene Damage Prediction

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

Gene ontology

• Biological process: muscle contraction;actin filament polymerization;myofibril assembly;positive regulation of actin filament polymerization;actin nucleation;sarcomere organization;pointed-end actin filament capping
• Cellular component: striated muscle thin filament;actin filament;myofibril;sarcomere;M band
• Molecular function: actin binding;actin monomer binding;tropomyosin binding