TCEANC2

transcription elongation factor A N-terminal and central domain containing 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:54053584-54112519

Previous symbols: [ "C1orf83" ]

Links

ENSG00000116205 ∙ NCBI:127428 ∙ ∙ HGNC:26494 ∙ Uniprot:Q96MN5 ∙ 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 TCEANC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEANC2 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			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	0	0

Variants in TCEANC2

This is a list of pathogenic ClinVar variants found in the TCEANC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-54054429-A-G		not specified	Uncertain significance (Dec 13, 2022)
1-54054445-C-A		not specified	Uncertain significance (Apr 06, 2024)
1-54068774-G-A		not specified	Uncertain significance (Mar 21, 2023)
1-54088603-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-54088681-T-C		not specified	Uncertain significance (May 10, 2024)
1-54088710-A-G		not specified	Uncertain significance (Aug 15, 2023)
1-54088711-T-C		not specified	Uncertain significance (Sep 20, 2023)
1-54088753-A-G		not specified	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEANC2	protein_coding	protein_coding	ENST00000234827	4	58933

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.76e-7	0.175	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.289	107	116	0.924	0.00000705	1332
Missense in Polyphen		30	35.467	0.84586		390
Synonymous	0.651	40	45.6	0.877	0.00000281	407
Loss of Function	-0.0232	10	9.92	1.01	5.67e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000911	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.000177	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.0295
• hipred: N
• hipred_score: 0.216
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tceanc2

Gene ontology

• Biological process: transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: protein binding