TKTL1

transketolase like 1

Basic information

Region (hg38): X:154295795-154330350

Links

ENSG00000007350 ∙ NCBI:8277 ∙ OMIM:300044 ∙ HGNC:11835 ∙ Uniprot:P51854 ∙ 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 TKTL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TKTL1 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						0
missense			23	1	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	1

Variants in TKTL1

This is a list of pathogenic ClinVar variants found in the TKTL1 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-154295882-C-T			Benign (May 30, 2017)
X-154295910-C-G		not specified	Uncertain significance (Jan 11, 2023)
X-154295948-G-A		not specified	Uncertain significance (Nov 17, 2022)
X-154295952-G-T		not specified	Uncertain significance (Mar 17, 2023)
X-154295969-G-T		not specified	Uncertain significance (Jun 11, 2021)
X-154295984-C-T		not specified	Uncertain significance (Sep 16, 2021)
X-154305383-C-G		not specified	Uncertain significance (Apr 17, 2024)
X-154309384-C-G		not specified	Uncertain significance (Apr 08, 2022)
X-154310858-A-G		not specified	Likely benign (Jan 25, 2023)
X-154310973-C-T		not specified	Uncertain significance (Mar 16, 2022)
X-154311142-G-A		not specified	Uncertain significance (Oct 02, 2023)
X-154312587-G-C		not specified	Uncertain significance (Jun 16, 2024)
X-154312606-G-A		not specified	Uncertain significance (May 13, 2024)
X-154312711-C-G		not specified	Uncertain significance (Dec 20, 2023)
X-154315207-C-T		not specified	Uncertain significance (May 07, 2024)
X-154315269-T-C		not specified	Uncertain significance (Feb 07, 2023)
X-154320778-G-A		not specified	Uncertain significance (May 14, 2024)
X-154320796-A-G		not specified	Uncertain significance (Mar 29, 2022)
X-154320815-T-G		not specified	Uncertain significance (Aug 03, 2022)
X-154320883-A-G		not specified	Uncertain significance (Apr 06, 2022)
X-154320904-G-T		not specified	Uncertain significance (Jul 12, 2023)
X-154323273-C-T		not specified	Uncertain significance (May 27, 2022)
X-154323303-C-T		not specified	Uncertain significance (May 13, 2024)
X-154323330-A-G		not specified	Uncertain significance (Sep 14, 2022)
X-154323333-C-A		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TKTL1	protein_coding	protein_coding	ENST00000369915	13	34677

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000673	124439	0	1	124440	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.845	309	270	1.14	0.0000227	3915
Missense in Polyphen		50	84.173	0.59401		1316
Synonymous	-2.82	143	106	1.35	0.00000955	1190
Loss of Function	4.25	0	21.1	0.00	0.00000169	312

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)	0.0000123	0.00000887
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate. {ECO:0000250}.
• Pathway: Pentose phosphate pathway - Homo sapiens (human);Pentose phosphate cycle;pentose phosphate pathway (non-oxidative branch);pentose phosphate pathway;Pentose phosphate pathway (Consensus)

Recessive Scores

• pRec: 0.261

Intolerance Scores

• loftool: 0.0286
• rvis_EVS: -0.91
• rvis_percentile_EVS: 10.03

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.347
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000520

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tktl1
• Phenotype: digestive/alimentary phenotype; immune system phenotype; normal phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: glucose catabolic process;thiamine metabolic process
• Cellular component: nucleus;cytoplasm
• Molecular function: transketolase activity;metal ion binding