NM_000546.6(TP53):c.584T>C (p.Ile195Thr) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jun 30, 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:: RCV000487386.8

Allele description [Variation Report for NM_000546.6(TP53):c.584T>C (p.Ile195Thr)]

NM_000546.6(TP53):c.584T>C (p.Ile195Thr)

Gene:

TP53:tumor protein p53 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.584T>C (p.Ile195Thr)

HGVS:

NC_000017.11:g.7674947A>G
NG_017013.2:g.17604T>C
NM_000546.6:c.584T>CMANE SELECT
NM_001126112.3:c.584T>C
NM_001126113.3:c.584T>C
NM_001126114.3:c.584T>C
NM_001126115.2:c.188T>C
NM_001126116.2:c.188T>C
NM_001126117.2:c.188T>C
NM_001126118.2:c.467T>C
NM_001276695.3:c.467T>C
NM_001276696.3:c.467T>C
NM_001276697.3:c.107T>C
NM_001276698.3:c.107T>C
NM_001276699.3:c.107T>C
NM_001276760.3:c.467T>C
NM_001276761.3:c.467T>C
NP_000537.3:p.Ile195Thr
NP_000537.3:p.Ile195Thr
NP_001119584.1:p.Ile195Thr
NP_001119585.1:p.Ile195Thr
NP_001119586.1:p.Ile195Thr
NP_001119587.1:p.Ile63Thr
NP_001119588.1:p.Ile63Thr
NP_001119589.1:p.Ile63Thr
NP_001119590.1:p.Ile156Thr
NP_001263624.1:p.Ile156Thr
NP_001263625.1:p.Ile156Thr
NP_001263626.1:p.Ile36Thr
NP_001263627.1:p.Ile36Thr
NP_001263628.1:p.Ile36Thr
NP_001263689.1:p.Ile156Thr
NP_001263690.1:p.Ile156Thr
LRG_321t1:c.584T>C
LRG_321:g.17604T>C
LRG_321p1:p.Ile195Thr
NC_000017.10:g.7578265A>G
NM_000546.4:c.584T>C
NM_000546.5:c.584T>C
P04637:p.Ile195Thr

Protein change:

I156T

Links:

UniProtKB: P04637#VAR_005951; dbSNP: rs760043106

NCBI 1000 Genomes Browser:

rs760043106

Molecular consequence:

NM_000546.6:c.584T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.584T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.584T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.584T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.188T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.188T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.188T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.467T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.467T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.467T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.107T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.107T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.107T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.467T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.467T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens small nucleolar RNA, C/D box 88C (SNORD88C), small nucleolar RNA
Homo sapiens small nucleolar RNA, C/D box 88C (SNORD88C), small nucleolar RNA
gi|96974949|ref|NR_003069.1|

Nucleotide
ig30a03.y1 HR85 islet Homo sapiens cDNA 5', mRNA sequence
ig30a03.y1 HR85 islet Homo sapiens cDNA 5', mRNA sequence
gi|17926785|gnl|dbEST|10656838|gb|B 45.1|

Nucleotide
Criteria for Determining Disability in Infants and Children: Failure to Thrive
Criteria for Determining Disability in Infants and Children: Failure to Thrive

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000568761	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 30, 2022)	germline	clinical testing	Citation Link,
SCV001906056	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001959237	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000568761

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jun 30, 2022)

germline

clinical testing

Citation Link,

SCV001906056

Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Pathogenic

germline

clinical testing

SCV001959237

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Pathogenic

germline

clinical testing

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000568761.7

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

Description

Published functional studies demonstrate a damaging effect: non-functional transactivation, loss of growth suppression activity (Kato et al., 2003; Yamada et al., 2009; Slovackova et al., 2010; Kotler et al., 2018); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17724467, 27059324, 10567903, 30720243, 12124823, 19405127, 27714481, 26534844, 29324801, 12826609, 20505364, 29979965, 15510160, 19930417, 27501770, 12700230, 26585234, 21484931, 22784333, 20118236, 29625052, 30840781, 11238194, 12509970, 7732013, 16322298)

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

From Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute - VKGL Data-share Consensus, SCV001906056.1

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

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

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001959237.1

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

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

Last Updated: Oct 8, 2024

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