TMOD2

tropomodulin 2, the group of Tropomodulins

Basic information

Region (hg38): 15:51751596-51816363

Links

ENSG00000128872 ∙ NCBI:29767 ∙ OMIM:602928 ∙ HGNC:11872 ∙ Uniprot:Q9NZR1 ∙ 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 TMOD2 gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMOD2 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in TMOD2

This is a list of pathogenic ClinVar variants found in the TMOD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-51766481-A-G		not specified	Uncertain significance (Jun 22, 2021)
15-51766493-G-A		not specified	Uncertain significance (Jan 23, 2024)
15-51768301-A-G		not specified	Uncertain significance (Nov 12, 2021)
15-51768319-G-A		not specified	Uncertain significance (Jan 22, 2024)
15-51768332-G-A		not specified	Uncertain significance (Dec 19, 2023)
15-51773751-G-A		not specified	Likely benign (Jan 04, 2022)
15-51773816-G-A		not specified	Uncertain significance (Aug 13, 2021)
15-51773828-C-A		not specified	Uncertain significance (Sep 29, 2023)
15-51776937-C-G		not specified	Uncertain significance (Apr 22, 2022)
15-51781124-A-T		not specified	Uncertain significance (Dec 19, 2022)
15-51782730-A-G		not specified	Uncertain significance (Dec 15, 2023)
15-51782775-C-G		not specified	Uncertain significance (Feb 10, 2023)
15-51782782-A-G		not specified	Uncertain significance (Feb 05, 2024)
15-51782786-G-T		not specified	Uncertain significance (Apr 22, 2022)
15-51782803-C-T		not specified	Uncertain significance (Jan 17, 2024)
15-51782826-A-G		not specified	Uncertain significance (May 05, 2023)
15-51798208-C-G		not specified	Uncertain significance (Oct 26, 2021)
15-51798239-C-G		not specified	Uncertain significance (Nov 15, 2021)
15-51798264-C-A		not specified	Uncertain significance (Jan 24, 2023)
15-51798285-T-G		not specified	Uncertain significance (Aug 14, 2023)
15-51806386-T-G		not specified	Uncertain significance (Dec 13, 2022)
15-51806403-G-T		not specified	Uncertain significance (Jan 23, 2023)
15-51806420-T-C		not specified	Uncertain significance (Aug 21, 2023)
15-51806459-A-G		not specified	Uncertain significance (Jul 12, 2023)
15-51808438-A-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMOD2	protein_coding	protein_coding	ENST00000249700	9	64808

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0196	0.977	125729	0	15	125744	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.391	169	184	0.919	0.00000904	2328
Missense in Polyphen		50	60.059	0.83252		781
Synonymous	0.778	59	67.1	0.879	0.00000340	658
Loss of Function	2.55	6	17.5	0.342	9.05e-7	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000164	0.000163
South Asian	0.0000327	0.0000327
Other	0.000163	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: 0.135

Intolerance Scores

• loftool: 0.291
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.336
• hipred: Y
• hipred_score: 0.558
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.234

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmod2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: muscle contraction;neuron-neuron synaptic transmission;nervous system development;learning or memory;myofibril assembly;positive regulation of G protein-coupled receptor signaling pathway;pointed-end actin filament capping
• Cellular component: striated muscle thin filament;myofibril;growth cone
• Molecular function: actin binding;tropomyosin binding