TNNC2

troponin C2, fast skeletal type, the group of Troponin complex subunits|EF-hand domain containing|Cilia and flagella associated

Basic information

Region (hg38): 20:45823213-45833745

Links

ENSG00000101470

∙ NCBI:7125 ∙ OMIM:191039 ∙ HGNC:11944 ∙ Uniprot:P02585 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

congenital myopathy 15 (Limited), mode of inheritance: AD
congenital myopathy 15 (Limited), mode of inheritance: Unknown
hypertrophic cardiomyopathy (No Known Disease Relationship), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital myopathy 15	AD	Musculoskeletal	Early recognition of the disease may enable neonatal and early-childhood ventilatory and related support	Musculoskeletal	33755597

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TNNC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNNC2 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			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in TNNC2

This is a list of pathogenic ClinVar variants found in the TNNC2 region.

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

Position	Phenotype	Significance	ClinVar
20-45823356-C-T	not specified	Uncertain significance (May 14, 2024)	3327645
20-45824048-T-G	not specified	Uncertain significance (Aug 08, 2023)	2616840
20-45824059-G-A	not specified	Uncertain significance (Jun 23, 2023)	2605882
20-45824125-T-C	not specified	Uncertain significance (Jun 16, 2024)	3327646
20-45824369-C-G	Congenital myopathy 15	Pathogenic (Jul 16, 2024)	1806475
20-45824546-T-A	not specified	Uncertain significance (Aug 01, 2022)	2304171
20-45824594-C-A	Congenital myopathy 15	Pathogenic (Jul 16, 2024)	1806474

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNNC2	protein_coding	protein_coding	ENST00000372555	6	10532

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0162	0.894	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	71	106	0.671	0.00000587	1094
Missense in Polyphen		24	42.338	0.56687		465
Synonymous	1.28	30	40.4	0.743	0.00000273	255
Loss of Function	1.42	4	8.47	0.472	3.59e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000819	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Troponin is the central regulatory protein of striated muscle contraction. Tn consists of three components: Tn-I which is the inhibitor of actomyosin ATPase, Tn-T which contains the binding site for tropomyosin and Tn-C. The binding of calcium to Tn-C abolishes the inhibitory action of Tn on actin filaments.;
Pathway: Calcium signaling pathway - Homo sapiens (human);Disopyramide Action Pathway;Procainamide (Antiarrhythmic) Action Pathway;Phenytoin (Antiarrhythmic) Action Pathway;Fosphenytoin (Antiarrhythmic) Action Pathway;Bopindolol Action Pathway;Timolol Action Pathway;Carteolol Action Pathway;Bevantolol Action Pathway;Practolol Action Pathway;Dobutamine Action Pathway;Isoprenaline Action Pathway;Arbutamine Action Pathway;Amiodarone Action Pathway;Levobunolol Action Pathway;Metipranolol Action Pathway;Mexiletine Action Pathway;Lidocaine (Antiarrhythmic) Action Pathway;Quinidine Action Pathway;Sotalol Action Pathway;Epinephrine Action Pathway;Betaxolol Action Pathway;Atenolol Action Pathway;Alprenolol Action Pathway;Acebutolol Action Pathway;Muscle/Heart Contraction;Diltiazem Action Pathway;Propranolol Action Pathway;Pindolol Action Pathway;Penbutolol Action Pathway;Oxprenolol Action Pathway;Metoprolol Action Pathway;Esmolol Action Pathway;Bisoprolol Action Pathway;Bupranolol Action Pathway;Nebivolol Action Pathway;Amlodipine Action Pathway;Verapamil Action Pathway;Nitrendipine Action Pathway;Nisoldipine Action Pathway;Nimodipine Action Pathway;Ibutilide Action Pathway;Tocainide Action Pathway;Flecainide Action Pathway;Isradipine Action Pathway;Nifedipine Action Pathway;Felodipine Action Pathway;Nadolol Action Pathway;Carvedilol Action Pathway;Labetalol Action Pathway;Striated Muscle Contraction;Striated Muscle Contraction;Muscle contraction (Consensus)

Recessive Scores

pRec: 0.270

Intolerance Scores

loftool: 0.351
rvis_EVS: -0.01
rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

pHI: 0.152
hipred: Y
hipred_score: 0.573
ghis: 0.604

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0541

Mouse Genome Informatics

Gene name: Tnnc2
Phenotype

Gene ontology

Biological process: skeletal muscle contraction;regulation of muscle contraction;muscle filament sliding
Cellular component: cytosol;troponin complex
Molecular function: actin binding;calcium ion binding;protein binding;calcium-dependent protein binding;actin filament binding