TMOD1

tropomodulin 1, the group of Tropomodulins

Basic information

Region (hg38): 9:97501179-97601743

Previous symbols: [ "D9S57E", "TMOD" ]

Links

ENSG00000136842 ∙ NCBI:7111 ∙ OMIM:190930 ∙ HGNC:11871 ∙ Uniprot:P28289 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMOD1 gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMOD1 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				1		1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in TMOD1

This is a list of pathogenic ClinVar variants found in the TMOD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-97546189-C-T		not specified	Uncertain significance (Dec 22, 2023)
9-97546204-G-C		not specified	Uncertain significance (May 31, 2022)
9-97546234-C-T		not specified	Uncertain significance (Jun 07, 2023)
9-97546240-C-T		not specified	Uncertain significance (Mar 29, 2023)
9-97564075-C-T			Likely benign (Sep 01, 2022)
9-97564115-C-T		Idiopathic cardiomyopathy	Uncertain significance (Mar 18, 2024)
9-97564126-C-G		not specified	Uncertain significance (Nov 15, 2021)
9-97565932-C-T		not specified	Uncertain significance (Dec 20, 2023)
9-97568912-A-G		not specified	Uncertain significance (Dec 01, 2023)
9-97568984-G-A		not specified	Uncertain significance (May 18, 2023)
9-97591400-G-A		not specified	Uncertain significance (Jun 29, 2022)
9-97591427-A-G		not specified	Uncertain significance (Oct 10, 2023)
9-97599652-C-T		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMOD1	protein_coding	protein_coding	ENST00000259365	9	100569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.478	0.521	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	160	210	0.761	0.0000120	2353
Missense in Polyphen		57	72.259	0.78883		809
Synonymous	-0.439	90	84.9	1.06	0.00000511	690
Loss of Function	3.18	4	19.0	0.211	0.00000105	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Blocks the elongation and depolymerization of the actin filaments at the pointed end. The Tmod/TM complex contributes to the formation of the short actin protofilament, which in turn defines the geometry of the membrane skeleton. May play an important role in regulating the organization of actin filaments by preferentially binding to a specific tropomyosin isoform at its N-terminus. {ECO:0000269|PubMed:8002995}.
• Pathway: Striated Muscle Contraction;Striated Muscle Contraction;Muscle contraction (Consensus)

Recessive Scores

• pRec: 0.235

Intolerance Scores

• loftool: 0.127
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.745
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.325

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmod1
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype

Gene ontology

• Biological process: muscle contraction;adult locomotory behavior;muscle filament sliding;myofibril assembly;pointed-end actin filament capping;lens fiber cell development
• Cellular component: cytosol;striated muscle thin filament;actin filament;COP9 signalosome;membrane;myofibril;sarcomere;cortical cytoskeleton
• Molecular function: actin binding;tropomyosin binding;actin filament binding