TCEAL3

protein-coding

transcription elongation factor A like 3, 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. Alternative splicing results in multiple transcript variants encoding a single isoform. [provided by RefSeq, Jul 2008]

MANE transcript

NM_032926.3

Inheritance

—

ClinVar variants

U:14B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:103,607,451-103,629,690

External References & Databases

Ensembl (ENSG00000196507)

Transcript & Mutation Effects

hg38 • Region Span ~22.2 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 TCEAL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 13

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032926.3. 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				1 clinvar		1
missense			12 clinvar	1 clinvar		13
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	14	2	0	16

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032926.3	RefSeq	NP_116315.1	1	MANE Select
ENST00000372627.10	Ensembl	ENSP00000361710.5	1	MANE Select
NM_001006933.2	RefSeq	NP_001006934.1	1	Standard
ENST00000243286.7	Ensembl	ENSP00000243286.3	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: ENST00000372628
Coding exons: 1
Length: 22240
Individuals with no LoFs: 125738
Homozygous LoFs: 1
Heterozygous LoFs: 1
Defined: 125740
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	54	81.8	0.660	0.00000676	1305
Missense (PolyPhen)		15	19.9	0.75378		364
Synonymous	0.869	27	33.4	0.809	0.00000301	357
Loss of Function	1.95	0	4.45	0.00	2.81e-7	91

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)	0.000024	0.000018	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: 0.102

Intolerance Scores

RVIS EVS: 0.21
RVIS percentile EVS: 67.72

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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