TMOD3

tropomodulin 3, the group of Tropomodulins

Basic information

Region (hg38): 15:51829628-51947295

Links

ENSG00000138594 ∙ NCBI:29766 ∙ OMIM:605112 ∙ HGNC:11873 ∙ Uniprot:Q9NYL9 ∙ 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 TMOD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMOD3 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						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in TMOD3

This is a list of pathogenic ClinVar variants found in the TMOD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-51862901-G-A		not specified	Uncertain significance (Aug 02, 2022)
15-51862958-C-T		not specified	Uncertain significance (Jul 13, 2021)
15-51869271-A-G		not specified	Uncertain significance (Sep 22, 2021)
15-51869359-C-G		not specified	Uncertain significance (Feb 13, 2023)
15-51889056-C-G		not specified	Uncertain significance (Mar 28, 2024)
15-51889112-A-G		not specified	Uncertain significance (May 25, 2022)
15-51893842-C-T		not specified	Uncertain significance (Dec 06, 2022)
15-51893850-G-A		not specified	Uncertain significance (Dec 13, 2023)
15-51893854-A-G		not specified	Uncertain significance (Jun 18, 2021)
15-51893871-A-G		not specified	Uncertain significance (Jul 06, 2021)
15-51896465-C-G		not specified	Uncertain significance (Nov 22, 2021)
15-51896471-C-T		not specified	Uncertain significance (Apr 15, 2024)
15-51896476-G-A		not specified	Uncertain significance (Mar 14, 2023)
15-51896488-A-G		not specified	Uncertain significance (Aug 08, 2023)
15-51896503-C-T		not specified	Uncertain significance (Oct 05, 2022)
15-51901907-A-G		not specified	Uncertain significance (Nov 07, 2022)
15-51938168-T-A		LEO1-related disorder	Likely benign (Jun 24, 2019)
15-51938221-C-T		not specified	Uncertain significance (Aug 13, 2021)
15-51938228-T-A			Uncertain significance (Oct 21, 2021)
15-51941565-C-A		LEO1-related disorder	Likely benign (Feb 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMOD3	protein_coding	protein_coding	ENST00000308580	9	117668

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0664	0.931	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.222	177	186	0.954	0.00000923	2340
Missense in Polyphen		46	60.174	0.76444		794
Synonymous	0.471	63	67.9	0.927	0.00000351	650
Loss of Function	2.63	5	16.5	0.302	7.91e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000553	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.00000883	0.00000879
Middle Eastern	0.0000553	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000173	0.000163

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 (By similarity). {ECO:0000250}.
• Pathway: Striated Muscle Contraction;Muscle contraction (Consensus)

Recessive Scores

• pRec: 0.195

Intolerance Scores

• loftool: 0.384
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.464
• hipred: Y
• hipred_score: 0.533
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.647

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmod3
• Phenotype: cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); liver/biliary system phenotype; hematopoietic system 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)

Gene ontology

• Biological process: muscle contraction;myofibril assembly;erythrocyte development;pointed-end actin filament capping;cell-cell adhesion;positive regulation of mitotic cell cycle phase transition
• Cellular component: striated muscle thin filament;cell-cell adherens junction;myofibril
• Molecular function: actin binding;tropomyosin binding;cadherin binding involved in cell-cell adhesion