TKTL2

transketolase like 2

Basic information

Region (hg38): 4:163471095-163473754

Links

ENSG00000151005 ∙ NCBI:84076 ∙ ∙ HGNC:25313 ∙ Uniprot:Q9H0I9 ∙ 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 TKTL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TKTL2 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			44	3		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	5	0

Variants in TKTL2

This is a list of pathogenic ClinVar variants found in the TKTL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-163471864-A-G		not specified	Uncertain significance (Jan 19, 2022)
4-163471997-C-G		not specified	Uncertain significance (Jan 23, 2024)
4-163472059-C-A		not specified	Uncertain significance (Apr 13, 2022)
4-163472063-C-T		not specified	Uncertain significance (Nov 08, 2022)
4-163472090-T-C		not specified	Uncertain significance (Sep 16, 2021)
4-163472101-T-A		not specified	Uncertain significance (Aug 10, 2021)
4-163472108-G-A		not specified	Uncertain significance (Apr 06, 2022)
4-163472132-C-T		not specified	Uncertain significance (Aug 19, 2023)
4-163472215-A-G		not specified	Uncertain significance (May 29, 2024)
4-163472237-G-A		not specified	Uncertain significance (Aug 02, 2022)
4-163472242-A-G		not specified	Uncertain significance (Sep 12, 2023)
4-163472312-G-C		not specified	Uncertain significance (Jun 16, 2024)
4-163472339-C-T		not specified	Uncertain significance (Feb 06, 2024)
4-163472381-G-A		not specified	Uncertain significance (Mar 17, 2023)
4-163472391-A-G			Likely benign (Dec 01, 2022)
4-163472410-C-T		not specified	Uncertain significance (May 24, 2023)
4-163472506-G-A		not specified	Uncertain significance (Sep 17, 2021)
4-163472546-A-C		not specified	Uncertain significance (Jun 05, 2023)
4-163472560-G-T		not specified	Uncertain significance (Apr 12, 2022)
4-163472576-T-C		not specified	Uncertain significance (Apr 22, 2022)
4-163472581-C-T		not specified	Uncertain significance (Sep 07, 2022)
4-163472587-C-T		not specified	Uncertain significance (Feb 16, 2023)
4-163472616-C-T		not specified	Uncertain significance (Mar 24, 2023)
4-163472618-T-C		not specified	Uncertain significance (Sep 21, 2023)
4-163472698-G-T		not specified	Uncertain significance (Oct 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TKTL2	protein_coding	protein_coding	ENST00000280605	1	2791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-7	0.569	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0459	374	377	0.993	0.0000214	4097
Missense in Polyphen		114	132.85	0.85811		1574
Synonymous	1.57	120	144	0.834	0.00000876	1299
Loss of Function	1.02	13	17.6	0.737	0.00000123	181

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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in total transketolase activity and cell proliferation in cancer cells; after transfection with anti-TKTL1 siRNA, total transketolase activity dramatically decreases and proliferation was significantly inhibited in cancer cells. Plays a pivotal role in carcinogenesis. {ECO:0000269|PubMed:17321041}.
• Pathway: Pentose phosphate pathway - Homo sapiens (human);Pentose phosphate cycle;pentose phosphate pathway (non-oxidative branch);pentose phosphate pathway (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.313
• rvis_EVS: -0.17
• rvis_percentile_EVS: 40.6

Haploinsufficiency Scores

• pHI: 0.300
• hipred: N
• hipred_score: 0.192
• ghis: 0.391

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.413

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tktl2

Gene ontology

• Cellular component: cytoplasm
• Molecular function: transketolase activity;metal ion binding