Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

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

Help
Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 3, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000255738.10
Variation ID:
255738
Description:
single nucleotide variant
Help

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

Allele ID
252360
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6p21.1
Genomic location
6: 42968332 (GRCh38) GRCh38 UCSC
6: 42936070 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.42936070G>A
NC_000006.12:g.42968332G>A
NG_008370.1:g.15912C>T
... more HGVS
Protein change
A549V, A461V
Other names
-
Canonical SPDI
NC_000006.12:42968331:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00938 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00195
Exome Aggregation Consortium (ExAC) 0.00238
1000 Genomes Project 0.00938
The Genome Aggregation Database (gnomAD) 0.00592
Trans-Omics for Precision Medicine (TOPMed) 0.00657
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00700
Links
ClinGen: CA3811273
dbSNP: rs115960224
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Mar 18, 2016 RCV000244237.3
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Sep 24, 2020 RCV000514084.6
Benign 2 criteria provided, multiple submitters, no conflicts May 28, 2019 RCV000987702.2
Benign 1 criteria provided, single submitter Dec 5, 2020 RCV001082436.2
Benign 1 no assertion criteria provided Jan 6, 2020 RCV001276733.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PEX6 - - GRCh38
GRCh37
621 639

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303461.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Mar 18, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000340676.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Aug 31, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610127.1
Submitted: (Oct 05, 2017)
Evidence details
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 4a (zellweger)
Allele origin: unknown
Mendelics
Accession: SCV001137121.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 4a (zellweger)
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001320382.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
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, … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorders, Zellweger syndrome spectrum
Allele origin: germline
Invitae
Accession: SCV001028401.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Sep 24, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001828754.1
Submitted: (Sep 03, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 30245029, 19105186, 20981092, 22995991)
Benign
(Jan 06, 2020)
no assertion criteria provided
Method: clinical testing
Zellweger syndrome
Allele origin: germline
Natera, Inc.
Accession: SCV001463261.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders. Yik WY Human mutation 2009 PMID: 19105186
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PEX6 - - - -

Text-mined citations for rs115960224...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2021