TCERG1L

transcription elongation regulator 1 like

Basic information

Region (hg38): 10:131092390-131311721

Links

ENSG00000176769 ∙ NCBI:256536 ∙ ∙ HGNC:23533 ∙ Uniprot:Q5VWI1 ∙ 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 TCERG1L gene.

• Inborn genetic diseases (33 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCERG1L 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				2		2
missense			31	4		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	31	7	0

Variants in TCERG1L

This is a list of pathogenic ClinVar variants found in the TCERG1L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-131093175-C-T		not specified	Uncertain significance (Oct 18, 2021)
10-131093202-C-T			Likely benign (Jun 04, 2018)
10-131093268-C-T		not specified	Uncertain significance (Aug 17, 2021)
10-131093276-C-G		not specified	Uncertain significance (May 24, 2023)
10-131093283-C-T		not specified	Uncertain significance (Aug 02, 2021)
10-131098331-G-C		not specified	Uncertain significance (Mar 07, 2024)
10-131098385-A-G		not specified	Uncertain significance (Oct 05, 2022)
10-131104329-T-C		not specified	Uncertain significance (Feb 28, 2023)
10-131104343-A-T		not specified	Uncertain significance (Mar 24, 2023)
10-131116837-G-A		not specified	Uncertain significance (Jun 01, 2023)
10-131116838-C-G		not specified	Uncertain significance (Dec 01, 2022)
10-131116863-G-A		not specified	Uncertain significance (Jul 06, 2021)
10-131116872-G-A		not specified	Uncertain significance (Oct 18, 2021)
10-131116889-C-T			Likely benign (May 17, 2018)
10-131116930-C-T		not specified	Uncertain significance (Nov 03, 2023)
10-131134385-C-T		not specified	Uncertain significance (Oct 02, 2023)
10-131146556-T-C		not specified	Uncertain significance (Jul 15, 2021)
10-131146634-C-T		not specified	Uncertain significance (Sep 12, 2023)
10-131163200-G-A		not specified	Uncertain significance (Feb 28, 2023)
10-131166826-T-G		not specified	Uncertain significance (Dec 06, 2022)
10-131166841-T-A		not specified	Uncertain significance (Jun 06, 2023)
10-131166847-C-G		not specified	Uncertain significance (Sep 21, 2023)
10-131166855-C-T		not specified	Uncertain significance (Sep 01, 2021)
10-131260250-C-T			Likely benign (May 25, 2018)
10-131260265-C-T		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCERG1L	protein_coding	protein_coding	ENST00000368642	12	219331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.84e-9	0.684	125570	0	39	125609	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.466	241	262	0.919	0.0000158	3704
Missense in Polyphen		70	93.599	0.74787		1080
Synonymous	0.706	98	107	0.913	0.00000689	1216
Loss of Function	1.33	16	22.8	0.700	0.00000140	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000762	0.000735
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.0000547	0.0000544
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000107	0.000106
Middle Eastern	0.0000547	0.0000544
South Asian	0.000273	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0933

Intolerance Scores

• loftool: 0.965
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.61

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.267
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcerg1l

Gene ontology

• Cellular component: nucleus