79419-8

PMS2 gene deletion+duplication and full mutation analysis in Blood or Tissue by Molecular genetics method

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Term Description

The coding sequences of PMS2 are amplified by polymerase chain reaction and each PCR product (amplicon) then sequences bidirectionally using Sanger sequencing methodology. The multiple-ligation-probe amplification assay (MLPA) was performed to detect copy number variations (deletions and duplications) in the PMS2 gene. Exact breakpoints are not determined for any large deletions or duplications detected by this analysis.

Part Description

LP199719-8 PMS2 gene
The PMS2 gene (PMS1 homolog 2, mismatch repair system component) [HGNC Gene ID:9122] is located on chromosome 7p22.1. This gene is one of the PMS2 gene family members found in clusters on chromosome 7. The product of this gene is involved in DNA mismatch repair. It forms a heterodimer with MLH1 and this complex interacts with other complexes bound to mismatched bases. Mutations in this gene are associated with hereditary nonpolyposis colorectal cancer (also known as Lynch syndrome), Turcot syndrome, and are a cause of supratentorial primitive neuroectodermal tumors. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2008] [NCBI Gene ID: 5395] Source: National Center for Biotechnology Information (NCBI) Gene

LOINC Names Get Info

Fully-Specified Name: PMS2 gene deletion+duplication & full mutation analysis:Find:Pt:Bld/Tiss:Doc:Molgen
Long Common Name: PMS2 gene deletion+duplication and full mutation analysis in Blood or Tissue by Molecular genetics method
Short Name: PMS2 gene Del+Dup + Full Mut Anl Bld/T
Display Name: PMS2 gene del+dup and full mutation analysis Molgen Doc (Bld/Tiss)
Consumer Name Alpha Get Info: PMS2 gene variant analysis, Blood or tissue specimen

Part Model Get Info

Component
PMS2 gene deletion+duplication & full mutation analysis
LP229359-7
- Analyte
  PMS2 gene deletion+duplication & full mutation analysis
  LP229359-7
  - Component Numerator
    PMS2 gene deletion+duplication & full mutation analysis
    LP229359-7
    - Component Numerator Core
      PMS2 gene
      LP199719-8
    - Component Numerator Core Suffix
      deletion+duplication & full mutation analysis
      LP200206-3
  - Component Denominator
    NULL
    - Component Denominator Core
      NULL
    - Component Denominator Core Suffix
      NULL
- Challenge
  NULL
- Adjustment
  NULL
- Count
  NULL
Property
Find
LP6813-2
Time
Pt
LP6960-1
- Time Core
  Pt
  LP6960-1
- Time Modifier
  NULL
System
Bld/Tiss
LP7061-7
- System Core
  Bld/Tiss
  LP7061-7
- Super System
  NULL
Scale
Doc
LP32888-7
Method
Molgen
LP6404-0

Associated Observations

81247-9 Master HL7 genetic variant reporting panel

LOINC	Name	R/O/C	Cardinality	Example UCUM Units
81247-9	Master HL7 genetic variant reporting panel
Indent81306-3	Variables that apply to the overall study
IndentIndent53577-3	Reason for study	O	0..*
IndentIndent51967-8	Genetic disease assessed [ID]	O	0..*
IndentIndent51963-7	Medication assessed [ID]	C	0..*
IndentIndent48018-6	Gene studied [ID]	C	0..*
IndentIndent36908-2	Gene mutations tested for in Blood or Tissue by Molecular genetics method Nominal	C	0..*
IndentIndent51959-5	Range(s) of DNA sequence examined	C	0..*
IndentIndent81293-3	Description of ranges of DNA sequences examined	C	0..1
IndentIndent51968-6	Discrete variation analysis overall interpretation	R	1..1
IndentIndent83006-7	Deletion-duplication overall interpretation	C
IndentIndent51969-4	Genetic analysis report	O	0..1
IndentIndent81291-7	Variant ISCN	C
IndentIndent62374-4	Human reference sequence assembly version	C	0..1
IndentIndent81303-0	HGVS version [ID]	O	0..1
IndentIndent82115-7	dbSNP version [ID]	O	0..1
IndentIndent83007-5	COSMIC version [ID]	O
IndentIndent83008-3	ClinVar version [ID]	O
Indent81250-3	Discrete genetic variant panel		0..n
IndentIndent83005-9	Variant category
IndentIndent81252-9	Discrete genetic variant	C	0..1
IndentIndent48018-6	Gene studied [ID]	C	0..1
IndentIndent51958-7	Transcript reference sequence [ID]	C	0..1
IndentIndent48004-6	DNA change (c.HGVS)	C	0..1
IndentIndent48005-3	Amino acid change (pHGVS)	C	0..1
IndentIndent48019-4	DNA change type	O	0..1
IndentIndent48006-1	Amino acid change [Type]	O	0..1
IndentIndent48013-7	Genomic reference sequence [ID]	C	0..1
IndentIndent81290-9	Genomic DNA change (gHGVS)	C
IndentIndent69547-8	Genomic ref allele [ID]	C	0..1
IndentIndent81254-5	Genomic allele start-end	C	0..1
IndentIndent69551-0	Genomic alt allele [ID]	C	0..1
IndentIndent84414-2	Haplotype name	O
IndentIndent81255-2	dbSNP [ID]	O	0..1
IndentIndent81257-8	CIGAR [ID]	O	0..1
IndentIndent48001-2	Cytogenetic (chromosome) location	O	0..1
IndentIndent48002-0	Genomic source class [Type]	O	0..1
IndentIndent81304-8	Variant analysis method [Type]	O
IndentIndent53037-8	Genetic variation clinical significance [Imp]	O	0..1
IndentIndent69548-6	Genetic variant assessment	O
IndentIndent81259-4	Associated phenotype	O	0..1
IndentIndent53034-5	Allelic state	C	0..1
IndentIndent81258-6	Sample variant allelic frequency [NFr]	O	0..1	%
IndentIndent82121-5	Allelic read depth	O	0..1	{#}
IndentIndent82120-7	Allelic phase	O	0..1
IndentIndent82309-6	Basis for allelic phase [Type]	O
Indent81297-4	Structural variant panel
IndentIndent82155-3	Genomic structural variant copy number			{#}
IndentIndent81299-0	Structural variant reported arrCGH [Ratio]	C	0..1	{Ratio}
IndentIndent81300-6	Structural variant [Length]	O	0..1	{#}
IndentIndent81301-4	Structural variant outer start and end	O	0..1	{Range}
IndentIndent81302-2	Structural variant inner start and end	O	0..1	{Range}
Indent81251-1	Complex genetic variant panel		0..n
IndentIndent81260-2	Complex genetic variant [ID]	C	0..1
IndentIndent81262-8	Complex variant HGVS name	C	0..1
IndentIndent81263-6	Complex variant type	C	0..1
IndentIndent81259-4	Associated phenotype	O	0..1
IndentIndent53037-8	Genetic variation clinical significance [Imp]	O	0..1
IndentIndent53034-5	Allelic state	O	0..1
IndentIndent82309-6	Basis for allelic phase [Type]	O
IndentIndent81250-3	Discrete genetic variant panel		0..n
IndentIndentIndent83005-9	Variant category
IndentIndentIndent81252-9	Discrete genetic variant	C	0..1
IndentIndentIndent48018-6	Gene studied [ID]	C	0..1
IndentIndentIndent51958-7	Transcript reference sequence [ID]	C	0..1
IndentIndentIndent48004-6	DNA change (c.HGVS)	C	0..1
IndentIndentIndent48005-3	Amino acid change (pHGVS)	C	0..1
IndentIndentIndent48019-4	DNA change type	O	0..1
IndentIndentIndent48006-1	Amino acid change [Type]	O	0..1
IndentIndentIndent48013-7	Genomic reference sequence [ID]	C	0..1
IndentIndentIndent81290-9	Genomic DNA change (gHGVS)	C
IndentIndentIndent69547-8	Genomic ref allele [ID]	C	0..1
IndentIndentIndent81254-5	Genomic allele start-end	C	0..1
IndentIndentIndent69551-0	Genomic alt allele [ID]	C	0..1
IndentIndentIndent84414-2	Haplotype name	O
IndentIndentIndent81255-2	dbSNP [ID]	O	0..1
IndentIndentIndent81257-8	CIGAR [ID]	O	0..1
IndentIndentIndent48001-2	Cytogenetic (chromosome) location	O	0..1
IndentIndentIndent48002-0	Genomic source class [Type]	O	0..1
IndentIndentIndent81304-8	Variant analysis method [Type]	O
IndentIndentIndent53037-8	Genetic variation clinical significance [Imp]	O	0..1
IndentIndentIndent69548-6	Genetic variant assessment	O
IndentIndentIndent81259-4	Associated phenotype	O	0..1
IndentIndentIndent53034-5	Allelic state	C	0..1
IndentIndentIndent81258-6	Sample variant allelic frequency [NFr]	O	0..1	%
IndentIndentIndent82121-5	Allelic read depth	O	0..1	{#}
IndentIndentIndent82120-7	Allelic phase	O	0..1
IndentIndentIndent82309-6	Basis for allelic phase [Type]	O
Indent82118-1	Pharmacogenomics result panel
IndentIndent48018-6	Gene studied [ID]		1..*
IndentIndent84413-4	Genotype display name
IndentIndent53040-2	Genetic variation's effect on drug metabolism	C	0..1
IndentIndent51961-1	Genetic variation's effect on drug efficacy	C	0..1
IndentIndent83009-1	Genetic variation's effect on high-risk allele
IndentIndent82117-3	Medication usage implications panel	O	0..*
IndentIndentIndent51963-7	Medication assessed [ID]	R	1..*
IndentIndentIndent82116-5	Medication usage suggestion [Type]	C	1..1
IndentIndentIndent83010-9	Medication usage suggestion [Narrative]	C
Indent83011-7	Haplotype definition panel
IndentIndent48018-6	Gene studied [ID]	C	0..1
IndentIndent84414-2	Haplotype name	O
IndentIndent81250-3	Discrete genetic variant panel		0..n
IndentIndentIndent83005-9	Variant category
IndentIndentIndent81252-9	Discrete genetic variant	C	0..1
IndentIndentIndent48018-6	Gene studied [ID]	C	0..1
IndentIndentIndent51958-7	Transcript reference sequence [ID]	C	0..1
IndentIndentIndent48004-6	DNA change (c.HGVS)	C	0..1
IndentIndentIndent48005-3	Amino acid change (pHGVS)	C	0..1
IndentIndentIndent48019-4	DNA change type	O	0..1
IndentIndentIndent48006-1	Amino acid change [Type]	O	0..1
IndentIndentIndent48013-7	Genomic reference sequence [ID]	C	0..1
IndentIndentIndent81290-9	Genomic DNA change (gHGVS)	C
IndentIndentIndent69547-8	Genomic ref allele [ID]	C	0..1
IndentIndentIndent81254-5	Genomic allele start-end	C	0..1
IndentIndentIndent69551-0	Genomic alt allele [ID]	C	0..1
IndentIndentIndent84414-2	Haplotype name	O
IndentIndentIndent81255-2	dbSNP [ID]	O	0..1
IndentIndentIndent81257-8	CIGAR [ID]	O	0..1
IndentIndentIndent48001-2	Cytogenetic (chromosome) location	O	0..1
IndentIndentIndent48002-0	Genomic source class [Type]	O	0..1
IndentIndentIndent81304-8	Variant analysis method [Type]	O
IndentIndentIndent53037-8	Genetic variation clinical significance [Imp]	O	0..1
IndentIndentIndent69548-6	Genetic variant assessment	O
IndentIndentIndent81259-4	Associated phenotype	O	0..1
IndentIndentIndent53034-5	Allelic state	C	0..1
IndentIndentIndent81258-6	Sample variant allelic frequency [NFr]	O	0..1	%
IndentIndentIndent82121-5	Allelic read depth	O	0..1	{#}
IndentIndentIndent82120-7	Allelic phase	O	0..1
IndentIndentIndent82309-6	Basis for allelic phase [Type]	O

Basic Attributes

Class: MOLPATH
Type: Laboratory
First Released: Version 2.54
Last Updated: Version 2.73 (MIN)
Order vs. Observation: Both
Common Test Rank Get Info: 18104

Language Variants Get Info

Tag	Language	Translation
cs-CZ	Czech (Czechia)	Gen PMS2 delece+duplikace a kompletní mutační analýza:Nález:Časový bod:Krev/tkáň:Dokument:Molekulární genetika
el-GR	Greek (Greece)	Γονίδιο PMS2 ανάλυση διαγραφής+διπλασιασμού & πλήρους μετάλλαξης:Εύρεση:Pt:Αίμα/Ιστός:Doc:Μοριακή γενετική Synonyms: Doc MOLPATH Pt Αίμα Αίμα/Ιστός ανάλυση διαγραφής+διπλασιασμού & πλήρους μετάλλαξης Γονίδιο Γονίδιο PMS2 διαγραφή διαγραφή+διπλασιασμός διπλασιασμός Εύρεση Ιστός Μοριακή γενετική πλήρης ανάλυση μεταλλάξεων
es-ES	Spanish (Spain)	Gen PMS2 estudio delecion+duplicacion y estudio mutacional completo:Hallazgo:Punto temporal:Sangre o tejido:Doc:Genética molecular
es-MX	Spanish (Mexico)	Eliminación del gen PMS2 + duplicación y análisis de mutación completo:Hallazgo:Punto temporal:Sangre o tejido:Documento:Genética molecular
fr-FR	French (France)	PMS2 gène délétion+duplication et analyse complète des mutations:Recherche:Ponctuel:Sang/Tissu:Document:Biologie moléculaire
it-IT	Italian (Italy)	PMS2, gene Delezione+duplicazione & analisi di mutazione completa:Osservazione:Pt:Sangue/Tess:Doc:Molgen Synonyms: delezione e duplicazione Gene PMS2 Genetica molecolare Osservazione Patologia molecolare Punto nel tempo (episodio) Sangue Sangue o Tessuto Tessuto & Strisci
nl-NL	Dutch (Netherlands)	PMS2-gen deletie + duplicatie & volledige mutatie analyse:bevinding:moment:bloed of weefsel:document:moleculair genetisch onderzoek Synonyms: molgen PMS2 gen
pl-PL	Polish (Poland)	PMS2 gen delecja+duplikacja i pełna analiza mutacji:stwierdzenie:punkt w czasie:krew lub tkanka:dokument:genetyka molekularna Synonyms: diagnostyka molekularna Gen PMS2
tr-TR	Turkish (Turkey)	PMS2 geni delesyon+duplikasyon ve tam mutasyon analizi:Bulgu:Zmlı:Kan/Dk:Dokm:Molgen Synonyms: çiftleme
zh-CN	Chinese (China)	PMS2 基因缺失+重复与全面的突变分析:发现:时间点:全血/组织:文档型:分子遗传学类实验室方法 Synonyms: 临床文档型;临床文档;文档;文书;医疗文书;临床医疗文书全血或组织;血液/组织;血液或组织分子病理学;分子病理学试验分子遗传学;分子遗传学方法;分子遗传学类方法;分子遗传学类检验方法;包括 RFL、PCR 及其他方法在内，用于在分子基础上检测遗传属性的方法的大类;聚合酶链反应;聚合酶链式反应发现是一个原子型临床观察指标，并不是作为印象的概括陈述。体格检查、病史、系统检查及其他此类观察指标的属性均为发现。它们的标尺对于编码型发现可能是名义型，而对于叙述型文本之中所报告的发现，则可能是叙述型。;发现物;所见;结果;结论基因复制;基因重复;重复基因缺失（基因缺失、缺损、基因缺损、基因删除、删除、基因丢失）+重复（基因重复）;基因缺失+重复完整突变分析;综合突变分析时刻;随机;随意;瞬间未作说明的组织;组织;组织 & 涂片染色体缺失;染色体区带缺失;基因缺失;缺损;基因缺损;基因删除;删除;基因丢失缺失（基因缺失、缺损、基因缺损、基因删除、删除、基因丢失）+重复（基因重复、重复基因、重复型基因、复制型基因）与全面的突变分析（突变全面分析、完整的突变分析、彻底的突变分析、全面型突变分析、全面式突变分析、突变全分析、突变彻底分析、全面突变分析）血;血液遗传基因;遗传因子;吉恩;生物基因错配修复核酸内切酶 PMS2;Mismatch repair endonuclease PMS2;PMS2;HNPCC4;MLH4;PMS2CL;PMSL2

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Copyright © Regenstrief Institute, Inc. All Rights Reserved. To the extent included herein, the LOINC table and LOINC codes are copyright © Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee. See https://loinc.org/license for the full LOINC copyright and license.