TCEAL6

transcription elongation factor A like 6, the group of Transcription elongation factor A like family

Basic information

Region (hg38): X:102140476-102142970

Links

ENSG00000204071 ∙ NCBI:158931 ∙ ∙ HGNC:24553 ∙ Uniprot:Q6IPX3 ∙ 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 TCEAL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEAL6 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	0

Variants in TCEAL6

This is a list of pathogenic ClinVar variants found in the TCEAL6 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-102140913-A-G		not specified	Uncertain significance (Apr 13, 2023)
X-102140952-T-A		not specified	Uncertain significance (Oct 04, 2024)
X-102140953-C-T		not specified	Uncertain significance (Oct 04, 2024)
X-102140958-G-C		not specified	Uncertain significance (Oct 04, 2024)
X-102140975-G-T		not specified	Uncertain significance (Oct 06, 2023)
X-102140982-C-T		not specified	Uncertain significance (Aug 05, 2024)
X-102140985-C-T		not specified	Uncertain significance (Sep 26, 2022)
X-102141019-A-T		not specified	Uncertain significance (Nov 24, 2024)
X-102141022-C-T		not specified	Uncertain significance (Jun 06, 2023)
X-102141030-G-C		not specified	Uncertain significance (Mar 25, 2024)
X-102141058-C-T		not specified	Likely benign (Oct 10, 2023)
X-102141120-T-C		not specified	Uncertain significance (Jun 07, 2023)
X-102141145-T-C		not specified	Likely benign (Sep 26, 2023)
X-102141181-C-T		not specified	Uncertain significance (Sep 03, 2024)
X-102141249-C-G		not specified	Uncertain significance (Oct 25, 2024)
X-102141291-T-A		not specified	Uncertain significance (Nov 08, 2024)
X-102141320-G-C			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEAL6	protein_coding	protein_coding	ENST00000372774	1	2495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0166	0.490	125732	2	1	125735	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.620	89	74.0	1.20	0.00000600	1196
Missense in Polyphen		11	13.752	0.7999		304
Synonymous	-0.144	33	32.0	1.03	0.00000296	324
Loss of Function	-0.544	2	1.32	1.51	8.33e-8	27

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.000157	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0784

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.0557
• hipred: N
• hipred_score: 0.158
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tceal6

Gene ontology

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