TCEANC

protein-coding

transcription elongation factor A N-terminal and central domain containing

Gene summary

Predicted to enable transcription elongation factor activity. Predicted to be involved in transcription elongation by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001297563.2

Inheritance

ClinVar variants

U:42B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chrX:13,653,112-13,681,964

External References & Databases

Ensembl (ENSG00000176896)

Transcript & Mutation Effects

hg38 • Region Span ~28.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

male infertility with azoospermia or oligozoospermia due to single gene mutationLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0018393

Submitter: King Faisal Specialist Hospital and Research Center

Alhathal et al., 2020 (PMID: 32719396) reported a missense variant in a large male infertility cohort (n=285 infertile man and case–control fertile man). Gene is scored according to ClinGen classification. Limited with total score of 3. Single variant segregation (3 points).

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TCEANC variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001297563.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			39 clinvar	6 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	42	7	0	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001297563.2	RefSeq	NP_001284492.1	1	MANE Select
ENST00000696128.1	Ensembl	ENSP00000512421.1	1	MANE Select
NM_001297564.2	RefSeq	NP_001284493.1	1	Standard
NM_152634.4	RefSeq	NP_689847.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transcription, DNA-templated

Molecular Function

protein binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000314720
Coding exons: 2
Length: 28859
Individuals with no LoFs: 124591
Homozygous LoFs: 11
Heterozygous LoFs: 24
Defined: 124626
p: 0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.280	108	117	0.927	0.00000808	2485
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00032	rare
Latino/Admixed American	0.00029	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000082	0.000056	rare
Finnish	0.000063	0.000046	rare
European (Non-Finnish)	0.00026	0.00018	rare
South Asian	0.000053	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.714
RVIS EVS: 0.68
RVIS percentile EVS: 84.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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