NM_000466.3(PEX1):c.1579A>G (p.Thr527Ala) AND Peroxisome biogenesis disorder 1B

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jul 14, 2021
Review status:: criteria provided, conflicting classifications

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:: RCV000660395.10

Allele description [Variation Report for NM_000466.3(PEX1):c.1579A>G (p.Thr527Ala)]

NM_000466.3(PEX1):c.1579A>G (p.Thr527Ala)

Gene:

PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q21.2

Genomic location:

Preferred name:

NM_000466.3(PEX1):c.1579A>G (p.Thr527Ala)

HGVS:

NC_000007.14:g.92510952T>C
NG_008341.2:g.22580A>G
NM_000466.3:c.1579A>GMANE SELECT
NM_001282677.2:c.1579A>G
NM_001282678.2:c.955A>G
NP_000457.1:p.Thr527Ala
NP_001269606.1:p.Thr527Ala
NP_001269607.1:p.Thr319Ala
NC_000007.13:g.92140266T>C
NG_008341.1:g.22580A>G
NM_000466.2:c.1579A>G

Protein change:

T319A

Links:

dbSNP: rs144942544

NCBI 1000 Genomes Browser:

rs144942544

Molecular consequence:

NM_000466.3:c.1579A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282677.2:c.1579A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282678.2:c.955A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Peroxisome biogenesis disorder 1B (PBD1B)
Synonyms:: Refsum disease, infantile form; Infantile Refsum disease; Infantile form of phytanic acid storage disease
Identifiers:: MONDO: MONDO:0011101; MedGen: C0282527; Orphanet: 44; OMIM: 601539

Recent activity

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PREDICTED: Centruroides sculpturatus dnaJ homolog subfamily B member 6-A-like (L...
PREDICTED: Centruroides sculpturatus dnaJ homolog subfamily B member 6-A-like (LOC111621244), transcript variant X3, mRNA
gi|1316133140|ref|XM_023363343.1|

Nucleotide
Clostridiales bacterium ORNL_2OR_SD_357
Clostridiales bacterium ORNL_2OR_SD_357
HMP reference genome

BioProject
PER2 [Nyctereutes procyonoides]
PER2 [Nyctereutes procyonoides]
Gene ID:129523451

Gene
ATP2A2 [Sapajus apella]
ATP2A2 [Sapajus apella]
Gene ID:116566800

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000782475	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 21, 2016)	maternal	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001806050	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 14, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000782475

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 21, 2016)

maternal

clinical testing

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

SCV001806050

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jul 14, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV000782475.1

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

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

From Genome-Nilou Lab, SCV001806050.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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