NM_000288.4(PEX7):c.653C>T (p.Ala218Val) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Dec 1, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000656252.17

Allele description [Variation Report for NM_000288.4(PEX7):c.653C>T (p.Ala218Val)]

NM_000288.4(PEX7):c.653C>T (p.Ala218Val)

Gene:

PEX7:peroxisomal biogenesis factor 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q23.3

Genomic location:

Preferred name:

NM_000288.4(PEX7):c.653C>T (p.Ala218Val)

HGVS:

NC_000006.12:g.136869909C>T
NG_008462.1:g.52330C>T
NM_000288.4:c.653C>TMANE SELECT
NP_000279.1:p.Ala218Val
NC_000006.11:g.137191047C>T
NM_000288.3:c.653C>T
O00628:p.Ala218Val

Protein change:

A218V; ALA218VAL

Links:

UniProtKB: O00628#VAR_007726; OMIM: 601757.0002; dbSNP: rs121909151

NCBI 1000 Genomes Browser:

rs121909151

Molecular consequence:

NM_000288.4:c.653C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000778213	Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes	no assertion criteria provided	Pathogenic (Aug 26, 2016)	germline	clinical testing
SCV001781986	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jan 28, 2021)	germline	clinical testing	Citation Link,
SCV002062702	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Dec 1, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000778213

Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes

no assertion criteria provided

Pathogenic
(Aug 26, 2016)

germline

clinical testing

SCV001781986

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jan 28, 2021)

germline

clinical testing

Citation Link,

SCV002062702

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Dec 1, 2021)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes, SCV000778213.1

#	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 GeneDx, SCV001781986.1

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

Description

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); 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: 31589614, 12325024, 10083738, 11756410, 9090381, 11781871)

#	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 CeGaT Center for Human Genetics Tuebingen, SCV002062702.14

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

Last Updated: Apr 15, 2024

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