NM_001953.5(TYMP):c.245dup (p.Met83fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 20, 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:: RCV002880462.3

Allele description [Variation Report for NM_001953.5(TYMP):c.245dup (p.Met83fs)]

NM_001953.5(TYMP):c.245dup (p.Met83fs)

Genes:

LOC130067864:ATAC-STARR-seq lymphoblastoid active region 19325 [Gene]
TYMP:thymidine phosphorylase [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_001953.5(TYMP):c.245dup (p.Met83fs)

HGVS:

NC_000022.11:g.50529311dup
NG_011860.1:g.5778dup
NG_016235.1:g.2132dup
NM_001113755.3:c.245dup
NM_001113756.3:c.245dup
NM_001257988.1:c.245dup
NM_001257989.1:c.245dup
NM_001953.5:c.245dupMANE SELECT
NP_001107227.1:p.Met83fs
NP_001107228.1:p.Met83fs
NP_001244917.1:p.Met83fs
NP_001244918.1:p.Met83fs
NP_001944.1:p.Met83fs
LRG_727t1:c.245dup
LRG_727t2:c.245dup
LRG_727:g.5778dup
LRG_727p1:p.Met83fs
LRG_727p2:p.Met83fs
NC_000022.10:g.50967736_50967737insC
NC_000022.10:g.50967740dup

Protein change:

M83fs

Molecular consequence:

NM_001113755.3:c.245dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001113756.3:c.245dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257988.1:c.245dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257989.1:c.245dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001953.5:c.245dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003230188	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 20, 2022)	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

SCV003230188

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 20, 2022)

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, SCV003230188.2

#	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.Met83Hisfs*41) 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

ClinVar

Relating variation to medicine