TCEAL2

protein-coding

transcription elongation factor A like 2, the group of Transcription elongation factor A like family

Gene summary

This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family contain TFA domains and may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. Multiple family members are located on the X chromosome. [provided by RefSeq, Jul 2008]

MANE transcript

NM_080390.4

Inheritance

—

ClinVar variants

U:19B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:102,125,679-102,140,426

External References & Databases

Ensembl (ENSG00000184905)

Transcript & Mutation Effects

hg38 • Region Span ~14.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TCEAL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080390.4. 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		2
missense			19 clinvar	4 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	19	6	0	25

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080390.4	RefSeq	NP_525129.1	1	MANE Select
ENST00000372780.6	Ensembl	ENSP00000361866.1	1	MANE Select
ENST00000329035.2	Ensembl	ENSP00000332359.2	1	Standard
ENST00000329035.3	Ensembl	ENSP00000332359.2	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

WW domain binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372780
Coding exons: 1
Length: 2024
Individuals with no LoFs: 120000
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 120001
p: 0.00000417

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.115	80	83.0	0.964	0.00000588	1500
Missense (PolyPhen)		9	11.155	0.80681		175
Synonymous	-1.71	43	30.9	1.39	0.00000247	391
Loss of Function	0.737	0	0.632	0.00	3.90e-8	17

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000013	0.0000094	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.0656

Intolerance Scores

LoFtool: 0.212
RVIS EVS: 0.44
RVIS percentile EVS: 77.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.888

Gene Damage Prediction

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