TC2N

tandem C2 domains, nuclear, the group of Synaptotagmin like tandem C2 proteins

Basic information

Region (hg38): 14:91779745-91867536

Previous symbols: [ "C14orf47", "MTAC2D1" ]

Links

ENSG00000165929 ∙ NCBI:123036 ∙ OMIM:619305 ∙ HGNC:19859 ∙ Uniprot:Q8N9U0 ∙ 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 TC2N gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TC2N 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			15
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	0	0

Variants in TC2N

This is a list of pathogenic ClinVar variants found in the TC2N region.

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

Position	Type	Phenotype	Significance	ClinVar
14-91783144-G-C		not specified	Uncertain significance (May 23, 2023)
14-91783156-T-C		not specified	Uncertain significance (Oct 03, 2023)
14-91783204-T-C		not specified	Uncertain significance (Mar 16, 2022)
14-91785235-C-A		not specified	Uncertain significance (Feb 17, 2023)
14-91785235-C-G		not specified	Uncertain significance (Sep 06, 2022)
14-91785245-G-A		not specified	Uncertain significance (Dec 19, 2022)
14-91785265-C-A		not specified	Uncertain significance (Oct 29, 2021)
14-91792375-T-C		not specified	Uncertain significance (Apr 27, 2023)
14-91792467-G-A		not specified	Uncertain significance (Oct 12, 2022)
14-91792539-G-A		not specified	Uncertain significance (Jan 23, 2024)
14-91797786-T-C		not specified	Uncertain significance (Oct 27, 2021)
14-91798336-T-G		not specified	Uncertain significance (Sep 17, 2021)
14-91799031-A-T		not specified	Uncertain significance (Jan 31, 2024)
14-91800333-C-A		not specified	Uncertain significance (Feb 21, 2024)
14-91800334-C-A		not specified	Uncertain significance (Feb 21, 2024)
14-91802295-C-T		not specified	Uncertain significance (Jan 04, 2022)
14-91802296-G-A		not specified	Uncertain significance (Feb 28, 2023)
14-91802298-C-T		not specified	Uncertain significance (Mar 04, 2024)
14-91802325-T-C		not specified	Uncertain significance (Nov 21, 2023)
14-91802329-T-C		not specified	Uncertain significance (May 30, 2023)
14-91802359-G-C		not specified	Uncertain significance (Mar 06, 2023)
14-91802364-T-C		not specified	Uncertain significance (Feb 06, 2024)
14-91812339-T-A		not specified	Uncertain significance (Jan 08, 2024)
14-91812413-G-A		not specified	Uncertain significance (Nov 08, 2022)
14-91812491-A-G		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TC2N	protein_coding	protein_coding	ENST00000435962	11	87786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-9	0.780	125636	0	112	125748	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.192	240	249	0.966	0.0000121	3189
Missense in Polyphen		68	73.169	0.92936		956
Synonymous	-0.831	96	86.2	1.11	0.00000419	930
Loss of Function	1.55	18	26.6	0.676	0.00000143	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000406	0.000401
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00116	0.00114
Finnish	0.00	0.00
European (Non-Finnish)	0.000573	0.000554
Middle Eastern	0.00116	0.00114
South Asian	0.000474	0.000457
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0922

Intolerance Scores

• loftool: 0.996
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.99

Haploinsufficiency Scores

• pHI: 0.0768
• hipred: N
• hipred_score: 0.465
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tc2n

Gene ontology

• Cellular component: cellular_component;nucleus
• Molecular function: molecular_function