TCEAL3

transcription elongation factor A like 3, the group of Transcription elongation factor A like family

Basic information

Region (hg38): X:103607451-103629690

Links

ENSG00000196507 ∙ NCBI:85012 ∙ ∙ HGNC:28247 ∙ Uniprot:Q969E4 ∙ 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 TCEAL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEAL3 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in TCEAL3

This is a list of pathogenic ClinVar variants found in the TCEAL3 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-103609089-G-C		not specified	Uncertain significance (Dec 04, 2024)
X-103609152-T-G		not specified	Uncertain significance (Aug 16, 2022)
X-103609158-G-A		not specified	Uncertain significance (Sep 30, 2021)
X-103609183-G-A		not specified	Uncertain significance (Jul 14, 2021)
X-103609219-G-A		not specified	Uncertain significance (Oct 19, 2024)
X-103609258-G-A		not specified	Uncertain significance (Nov 18, 2022)
X-103609366-C-T		not specified	Uncertain significance (Nov 11, 2024)
X-103609426-C-A		not specified	Uncertain significance (Jan 11, 2023)
X-103609574-G-A			Likely benign (Mar 01, 2022)
X-103609583-C-G		not specified	Uncertain significance (Sep 22, 2023)
X-103609609-G-A		not specified	Uncertain significance (Oct 12, 2024)
X-103609637-G-C		not specified	Uncertain significance (May 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEAL3	protein_coding	protein_coding	ENST00000372628	1	22240

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.740	0.250	125738	1	1	125740	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	54	81.8	0.660	0.00000676	1305
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000244	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.269
• ghis: 0.478

Essentials

• essential_gene_CRISPR: 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: Tceal3

Gene ontology

• Cellular component: nucleus
• Molecular function: WW domain binding