NM_001953.5(TYMP):c.331C>T (p.Gln111Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 15, 2023
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:: RCV003702690.2

Allele description [Variation Report for NM_001953.5(TYMP):c.331C>T (p.Gln111Ter)]

NM_001953.5(TYMP):c.331C>T (p.Gln111Ter)

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.331C>T (p.Gln111Ter)

HGVS:

NC_000022.11:g.50529222G>A
NG_011860.1:g.5864C>T
NG_016235.1:g.2218C>T
NG_202279.1:g.63G>A
NM_001113755.3:c.331C>T
NM_001113756.3:c.331C>T
NM_001257988.1:c.331C>T
NM_001257989.1:c.331C>T
NM_001953.5:c.331C>TMANE SELECT
NP_001107227.1:p.Gln111Ter
NP_001107228.1:p.Gln111Ter
NP_001244917.1:p.Gln111Ter
NP_001244918.1:p.Gln111Ter
NP_001944.1:p.Gln111Ter
LRG_727t1:c.331C>T
LRG_727t2:c.331C>T
LRG_727:g.5864C>T
LRG_727p1:p.Gln111Ter
LRG_727p2:p.Gln111Ter
NC_000022.10:g.50967651G>A

Protein change:

Q111*

Molecular consequence:

NM_001113755.3:c.331C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001113756.3:c.331C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001257988.1:c.331C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001257989.1:c.331C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001953.5:c.331C>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
SCV004465015	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 15, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9924029, 15781193, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004465015

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 15, 2023)

germline

clinical testing

PubMed (3)
[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 (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004465015.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with TYMP-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln111*) 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).

#	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: Sep 29, 2024

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