NM_001953.5(TYMP):c.112G>T (p.Glu38Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 17, 2024
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:: RCV003556264.1

Allele description [Variation Report for NM_001953.5(TYMP):c.112G>T (p.Glu38Ter)]

NM_001953.5(TYMP):c.112G>T (p.Glu38Ter)

Gene:

TYMP:thymidine phosphorylase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_001953.5(TYMP):c.112G>T (p.Glu38Ter)

Other names:

Gln>Ter

HGVS:

NC_000022.11:g.50529598C>A
NG_011860.1:g.5488G>T
NG_016235.1:g.1842G>T
NM_001113755.3:c.112G>T
NM_001113756.3:c.112G>T
NM_001257988.1:c.112G>T
NM_001257989.1:c.112G>T
NM_001953.5:c.112G>TMANE SELECT
NP_001107227.1:p.Glu38Ter
NP_001107228.1:p.Glu38Ter
NP_001244917.1:p.Glu38Ter
NP_001244918.1:p.Glu38Ter
NP_001944.1:p.Glu38Ter
LRG_727t1:c.112G>T
LRG_727t2:c.112G>T
LRG_727:g.5488G>T
LRG_727p1:p.Glu38Ter
LRG_727p2:p.Glu38Ter
NC_000022.10:g.50968027C>A
NM_001953.4:c.112G>T
c.112G>T

Protein change:

E38*

Links:

dbSNP: rs1054084896

NCBI 1000 Genomes Browser:

rs1054084896

Molecular consequence:

NM_001113755.3:c.112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001113756.3:c.112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001257988.1:c.112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001257989.1:c.112G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001953.5:c.112G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004300057	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 17, 2024)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 9924029, 15781193, 20585803, 28764801, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004300057

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 17, 2024)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

Thymidine phosphorylase gene mutations in MNGIE, a human mitochondrial disorder.

Nishino I, Spinazzola A, Hirano M.

Science. 1999 Jan 29;283(5402):689-92.

PubMed [citation]

PMID:: 9924029

Thymidine phosphorylase gene mutations in patients with mitochondrial neurogastrointestinal encephalomyopathy syndrome.

Slama A, Lacroix C, Plante-Bordeneuve V, Lombès A, Conti M, Reimund JM, Auxenfants E, Crenn P, Laforêt P, Joannard A, Seguy D, Pillant H, Joly P, Haut S, Messing B, Said G, Legrand A, Guiochon-Mantel A.

Mol Genet Metab. 2005 Apr;84(4):326-31. Epub 2005 Jan 24.

PubMed [citation]

PMID:: 15781193

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV004300057.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Glu38*) in the TYMP gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TYMP are known to be pathogenic (PMID: 9924029, 15781193). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This premature translational stop signal has been observed in individuals with mitochondrial neurogastrointestinal encephalomyopathy (PMID: 20585803, 28764801). ClinVar contains an entry for this variant (Variation ID: 223014). For these reasons, this variant has been classified as Pathogenic.

#	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: Mar 30, 2024

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