NM_022445.4(TPK1):c.174A>T (p.Gly58=) AND Childhood encephalopathy due to thiamine pyrophosphokinase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 13, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000650013.6

Allele description [Variation Report for NM_022445.4(TPK1):c.174A>T (p.Gly58=)]

NM_022445.4(TPK1):c.174A>T (p.Gly58=)

Gene:

TPK1:thiamin pyrophosphokinase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q35

Genomic location:

Preferred name:

NM_022445.4(TPK1):c.174A>T (p.Gly58=)

HGVS:

NC_000007.14:g.144682920T>A
NG_032112.2:g.158134A>T
NM_001042482.2:c.174A>T
NM_001350879.1:c.174A>T
NM_001350880.1:c.174A>T
NM_001350881.1:c.174A>T
NM_001350882.1:c.38A>T
NM_001350883.1:c.38A>T
NM_001350884.2:c.38A>T
NM_001350885.1:c.-133-34041A>T
NM_001350886.1:c.-223A>T
NM_001350887.1:c.-72A>T
NM_001350889.1:c.-60-59659A>T
NM_001350893.1:c.-133-34041A>T
NM_001350894.1:c.-72A>T
NM_001350895.1:c.-300A>T
NM_022445.4:c.174A>TMANE SELECT
NP_001035947.1:p.Gly58=
NP_001337808.1:p.Gly58=
NP_001337809.1:p.Gly58=
NP_001337810.1:p.Gly58=
NP_001337811.1:p.Glu13Val
NP_001337812.1:p.Glu13Val
NP_001337813.1:p.Glu13Val
NP_071890.2:p.Gly58=
NC_000007.13:g.144380013T>A
NM_022445.3:c.174A>T
NR_146934.1:n.218A>T
NR_146936.2:n.222A>T

Protein change:

E13V

Links:

dbSNP: rs1049396049

NCBI 1000 Genomes Browser:

rs1049396049

Molecular consequence:

NM_001350886.1:c.-223A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350887.1:c.-72A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350894.1:c.-72A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350895.1:c.-300A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350885.1:c.-133-34041A>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001350889.1:c.-60-59659A>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001350893.1:c.-133-34041A>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001350882.1:c.38A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350883.1:c.38A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001350884.2:c.38A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_146934.1:n.218A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146936.2:n.222A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001042482.2:c.174A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001350879.1:c.174A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001350880.1:c.174A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001350881.1:c.174A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_022445.4:c.174A>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Childhood encephalopathy due to thiamine pyrophosphokinase deficiency
Synonyms:: ENCEPHALOPATHY, EPISODIC, DUE TO THIAMINE PYROPHOSPHOKINASE DEFICIENCY; Thiamine metabolism dysfunction syndrome 5 (episodic encephalopathy type)
Identifiers:: MONDO: MONDO:0013761; MedGen: C3280866; Orphanet: 293955; OMIM: 614458

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000771850	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 13, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000771850

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 13, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000771850.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change affects codon 58 of the TPK1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the TPK1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TPK1-related conditions. ClinVar contains an entry for this variant (Variation ID: 540080). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 7, 2025

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