NM_000286.3(PEX12):c.182_184dup (p.Glu61_Ile62insLys) AND Peroxisome biogenesis disorder 3A (Zellweger)

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 6, 2022
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:: RCV001035823.7

Allele description [Variation Report for NM_000286.3(PEX12):c.182_184dup (p.Glu61_Ile62insLys)]

NM_000286.3(PEX12):c.182_184dup (p.Glu61_Ile62insLys)

Gene:

PEX12:peroxisomal biogenesis factor 12 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

17q12

Genomic location:

Preferred name:

NM_000286.3(PEX12):c.182_184dup (p.Glu61_Ile62insLys)

HGVS:

NC_000017.11:g.35577534_35577536dup
NG_008447.1:g.6102_6104dup
NM_000286.3:c.182_184dupMANE SELECT
NP_000277.1:p.Glu61_Ile62insLys
NC_000017.10:g.33904552_33904553insTTT
NC_000017.10:g.33904553_33904555dup
NM_000286.2:c.182_184dup
NM_000286.2:c.182_184dupAAA

Links:

dbSNP: rs1412916235

NCBI 1000 Genomes Browser:

rs1412916235

Molecular consequence:

NM_000286.3:c.182_184dup - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Name:: Peroxisome biogenesis disorder 3A (Zellweger)
Synonyms:: PEROXISOMAL BIOGENESIS DISORDER 3A (ZELLWEGER); Peroxisome biogenesis disorder 3A
Identifiers:: MONDO: MONDO:0013927; MedGen: C3553929; Orphanet: 912; OMIM: 614859

Recent activity

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ras-specific guanine nucleotide-releasing factor 2 [Rattus norvegicus]
ras-specific guanine nucleotide-releasing factor 2 [Rattus norvegicus]
gi|2000186027|ref|NP_446173.2|

Protein
PREDICTED: Mus musculus predicted gene, 40108 (Gm40108), ncRNA
PREDICTED: Mus musculus predicted gene, 40108 (Gm40108), ncRNA
gi|755567489|ref|XR_882402.1|

Nucleotide
Stropharia ambigua PBM2257 translation elongation factor 1-alpha (tef1) gene, pa...
Stropharia ambigua PBM2257 translation elongation factor 1-alpha (tef1) gene, partial cds
gi|300394645|gb|GU187756.1|

Nucleotide
Agaricomycetes 28S large subunit ribosomal RNA gene, partial sequence.
Agaricomycetes 28S large subunit ribosomal RNA gene, partial sequence.
PopSet: 300394361

PopSet
protein SPMIP9 [Homo sapiens]
protein SPMIP9 [Homo sapiens]
gi|22749357|ref|NP_689883.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001199161	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 6, 2022)	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

SCV001199161

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 6, 2022)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001199161.4

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

Description

This variant, c.182_184dup, results in the insertion of 1 amino acid(s) of the PEX12 protein (p.Glu61_Ile62insLys), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PEX12-related conditions. ClinVar contains an entry for this variant (Variation ID: 550849). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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