NM_000287.4(PEX6):c.1646C>T (p.Ala549Val) AND Peroxisome biogenesis disorder 4A (Zellweger)

Germline classification:: Benign (2 submissions)
Last evaluated:: May 28, 2019
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:: RCV000987702.5

Allele description [Variation Report for NM_000287.4(PEX6):c.1646C>T (p.Ala549Val)]

NM_000287.4(PEX6):c.1646C>T (p.Ala549Val)

Gene:

PEX6:peroxisomal biogenesis factor 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.1

Genomic location:

Preferred name:

NM_000287.4(PEX6):c.1646C>T (p.Ala549Val)

HGVS:

NC_000006.12:g.42968332G>A
NG_008370.1:g.15912C>T
NM_000287.4:c.1646C>TMANE SELECT
NM_001316313.2:c.1382C>T
NP_000278.3:p.Ala549Val
NP_001303242.1:p.Ala461Val
NC_000006.11:g.42936070G>A
NM_000287.3:c.1646C>T
NR_133009.2:n.1677C>T

Protein change:

A461V

Links:

dbSNP: rs115960224

NCBI 1000 Genomes Browser:

rs115960224

Molecular consequence:

NM_000287.4:c.1646C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001316313.2:c.1382C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_133009.2:n.1677C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Peroxisome biogenesis disorder 4A (Zellweger) (PBD4A)
Synonyms:: Zellweger syndrome spectrum (PEX6-related)
Identifiers:: MONDO: MONDO:0013930; MedGen: C3553936; Orphanet: 912; OMIM: 614862

Recent activity

Clear Turn Off Turn On

Vmn1r73 vomeronasal 1 receptor 73 [Mus musculus]
Vmn1r73 vomeronasal 1 receptor 73 [Mus musculus]
Gene ID:171237

Gene
Vmn1r73 AND (alive[prop]) (1)
Gene
corticoliberin preproprotein [Mus musculus]
corticoliberin preproprotein [Mus musculus]
gi|45429990|ref|NP_991338.1|

Protein

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
SCV001137121	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001320382	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 28, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001137121

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Benign
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV001320382

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 28, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders.

Yik WY, Steinberg SJ, Moser AB, Moser HW, Hacia JG.

Hum Mutat. 2009 Mar;30(3):E467-80. doi: 10.1002/humu.20932.

PubMed [citation]

PMID:: 19105186
PMCID:: PMC2649967

Details of each submission

From Mendelics, SCV001137121.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Illumina Laboratory Services, Illumina, SCV001320382.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

#	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: Aug 4, 2024

ClinVar

Relating variation to medicine