NM_000466.3(PEX1):c.2966T>C (p.Ile989Thr) AND multiple conditions

Germline classification:: Likely pathogenic (1 submission)
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:: RCV001004317.9

Allele description [Variation Report for NM_000466.3(PEX1):c.2966T>C (p.Ile989Thr)]

NM_000466.3(PEX1):c.2966T>C (p.Ile989Thr)

Genes:

GATAD1:GATA zinc finger domain containing 1 [Gene - OMIM - HGNC]
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.2966T>C (p.Ile989Thr)

HGVS:

NC_000007.14:g.92494357A>G
NG_008341.2:g.39175T>C
NM_000466.3:c.2966T>CMANE SELECT
NM_001282677.2:c.2795T>C
NM_001282678.2:c.2342T>C
NP_000457.1:p.Ile989Thr
NP_001269606.1:p.Ile932Thr
NP_001269607.1:p.Ile781Thr
NC_000007.13:g.92123671A>G
NG_008341.1:g.39175T>C
NM_000466.2:c.2966T>C

Protein change:

I781T

Links:

dbSNP: rs61750427

NCBI 1000 Genomes Browser:

rs61750427

Molecular consequence:

NM_000466.3:c.2966T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282677.2:c.2795T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282678.2:c.2342T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Peroxisome biogenesis disorder 1A (Zellweger) (PBD1A)
Synonyms:: Zellweger leukodystrophy; Peroxisome biogenesis disorder 1a
Identifiers:: MONDO: MONDO:0008953; MedGen: C4721541; OMIM: 214100

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001163198	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	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

SCV001163198

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

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	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 Baylor Genetics, SCV001163198.1

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

Last Updated: Nov 10, 2024

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