TCEANC

transcription elongation factor A N-terminal and central domain containing

Basic information

Region (hg38): X:13653112-13681964

Links

ENSG00000176896 ∙ NCBI:170082 ∙ OMIM:301084 ∙ HGNC:28277 ∙ Uniprot:Q8N8B7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Limited), mode of inheritance: XL

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEANC 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				1		1
missense			6	1		7
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	2	0

Variants in TCEANC

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

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

Position	Type	Phenotype	Significance	ClinVar
X-13662545-C-G		not specified	Uncertain significance (Jun 27, 2022)
X-13662777-C-T		not specified	Uncertain significance (May 13, 2024)
X-13662822-C-T		not specified	Likely benign (Jun 22, 2023)
X-13662997-G-A			Likely benign (May 01, 2022)
X-13663220-C-T		not specified	Uncertain significance (Mar 06, 2023)
X-13663254-C-G		not specified	Uncertain significance (Aug 12, 2022)
X-13663329-C-T		not specified	Uncertain significance (Nov 16, 2022)
X-13663403-C-T		not specified	Uncertain significance (Jun 05, 2023)
X-13663473-G-A		not specified	Uncertain significance (Oct 18, 2021)
X-13663479-C-T			Uncertain significance (Jun 01, 2024)
X-13663515-G-T		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEANC	protein_coding	protein_coding	ENST00000314720	2	28859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0519	0.869	124591	11	24	124626	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.280	108	117	0.927	0.00000808	2485
Missense in Polyphen		18	27.035	0.6658		642
Synonymous	0.503	40	44.3	0.904	0.00000335	700
Loss of Function	1.46	3	7.24	0.414	5.34e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000775	0.000609
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000817	0.0000556
Finnish	0.0000628	0.0000464
European (Non-Finnish)	0.000258	0.000177
Middle Eastern	0.0000817	0.0000556
South Asian	0.0000529	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.714
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.93

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tceanc

Gene ontology

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