LMOD1

leiomodin 1, the group of Leiomodins

Basic information

Region (hg38): 1:201896455-201946588

Links

ENSG00000163431 ∙ NCBI:25802 ∙ OMIM:602715 ∙ HGNC:6647 ∙ Uniprot:P29536 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• megacystis-microcolon-intestinal hypoperistalsis syndrome (Supportive), mode of inheritance: AD
• megacystis-microcolon-intestinal hypoperistalsis syndrome 3 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Megacystis-microcolon-intestinal hypoperistalsis syndrome 3	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary; Gastrointestinal; Renal	28292896

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMOD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMOD1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6		6
missense			28	2	2	32
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	28	9	3

Variants in LMOD1

This is a list of pathogenic ClinVar variants found in the LMOD1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-201899244-A-G			Uncertain significance (-)
1-201899314-G-A		not specified	Uncertain significance (Dec 19, 2022)
1-201899337-T-C		not specified	Uncertain significance (May 01, 2023)
1-201899382-G-T			Uncertain significance (-)
1-201899486-T-C			Likely benign (May 08, 2018)
1-201899509-C-T		not specified	Uncertain significance (Jul 12, 2023)
1-201899521-C-A		not specified	Uncertain significance (Oct 10, 2023)
1-201899533-CCTT-C			Likely benign (Jun 04, 2018)
1-201899580-C-T		Megacystis-microcolon-intestinal hypoperistalsis syndrome 3	Uncertain significance (Mar 25, 2024)
1-201899583-T-G		not specified	Uncertain significance (Mar 19, 2024)
1-201899591-C-G		not specified	Uncertain significance (Apr 13, 2022)
1-201899751-C-T		Megacystis-microcolon-intestinal hypoperistalsis syndrome 3	Pathogenic (May 20, 2021)
1-201899788-G-A		not specified	Uncertain significance (Apr 20, 2023)
1-201899900-G-A			Likely benign (May 25, 2018)
1-201899905-G-A		Visceral myopathy 1 • Megacystis-microcolon-intestinal hypoperistalsis syndrome 3	Pathogenic (Jun 02, 2021)
1-201899907-G-A		Megacystis-microcolon-intestinal hypoperistalsis syndrome 3	Pathogenic (May 20, 2021)
1-201899974-T-A		not specified	Uncertain significance (Mar 22, 2023)
1-201900004-C-T		not specified	Uncertain significance (Oct 16, 2023)
1-201900016-T-C		not specified	Uncertain significance (Dec 20, 2023)
1-201900018-A-G		not specified	Uncertain significance (Mar 02, 2023)
1-201900022-C-T		not specified	Uncertain significance (Oct 25, 2023)
1-201900130-T-A		not specified	Uncertain significance (Aug 12, 2022)
1-201900185-G-A			Likely benign (Jun 01, 2018)
1-201900318-G-A		not specified	Uncertain significance (Aug 10, 2021)
1-201900406-C-G		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMOD1	protein_coding	protein_coding	ENST00000367288	3	50136

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.871	0.129	124640	0	3	124643	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	271	332	0.816	0.0000185	3952
Missense in Polyphen		73	130.25	0.56046		1521
Synonymous	-0.966	147	133	1.11	0.00000774	1170
Loss of Function	3.17	2	15.5	0.129	9.25e-7	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates nucleation of actin filaments. {ECO:0000269|PubMed:26370058}.
• Pathway: Smooth Muscle Contraction;Muscle contraction (Consensus)

Recessive Scores

• pRec: 0.231

Intolerance Scores

• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• pHI: 0.289
• hipred: Y
• hipred_score: 0.570
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.167

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmod1

Gene ontology

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