VCV001535574.7 - ClinVar

NM_001351132.2(PEX5):c.1718+11_1718+14del

Germline

Classification

criteria provided, single submitter. Learn more about how ClinVar calculates review status.

Likely benign

This classification is based on the single submission received

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001351132.2(PEX5):c.1718+11_1718+14del

Variation ID: 1535574 Accession: VCV001535574.7

Type and length

Deletion, 4 bp

Location

Cytogenetic: 12p13.31 12: 7209848-7209851 (GRCh38) [ NCBI UCSC ] 12: 7362444-7362447 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 8, 2022	Feb 25, 2025	Oct 16, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001351132.2:c.1718+11_1718+14del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_000319.5:c.1694+11_1694+14del		intron variant
NM_001131023.2:c.1763+11_1763+14del		intron variant
NM_001131024.2:c.1607+11_1607+14del		intron variant
NM_001131025.2:c.1718+11_1718+14del		intron variant
NM_001131026.2:c.1718+11_1718+14del		intron variant
NM_001300789.3:c.1718+11_1718+14del		intron variant
NM_001351124.3:c.1607+11_1607+14del		intron variant
NM_001351126.2:c.1607+11_1607+14del		intron variant
NM_001351127.2:c.1607+11_1607+14del		intron variant
NM_001351128.2:c.1607+11_1607+14del		intron variant
NM_001351130.3:c.1607+11_1607+14del		intron variant
NM_001351131.2:c.1718+11_1718+14del		intron variant
NM_001351133.2:c.1718+11_1718+14del		intron variant
NM_001351134.2:c.1718+11_1718+14del		intron variant
NM_001351135.3:c.1652+11_1652+14del		intron variant
NM_001351136.2:c.1709+11_1709+14del		intron variant
NM_001351137.3:c.1607+11_1607+14del		intron variant
NM_001351138.2:c.1652+11_1652+14del		intron variant
NM_001351139.2:c.1583+11_1583+14del		intron variant
NM_001351140.2:c.1583+11_1583+14del		intron variant
NM_001374645.1:c.1607+11_1607+14del		intron variant
NM_001374646.1:c.1607+11_1607+14del		intron variant
NM_001374647.2:c.1718+11_1718+14del		intron variant
NM_001374648.2:c.1607+11_1607+14del		intron variant
NM_001374649.2:c.1583+11_1583+14del		intron variant
NC_000012.12:g.7209851_7209854del
NC_000012.11:g.7362447_7362450del
NG_008448.1:g.25689_25692del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000012.12:7209847:TATCTAT:TAT

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA6426556 dbSNP: rs749232654 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
PEX5		-	-	GRCh38 GRCh38 GRCh37	1073	1128

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Peroxisome biogenesis disorder 2B	Likely benign (1)	criteria provided, single submitter	Oct 16, 2024	RCV002090086.7

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	Expand all rows Collapse all rows Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely benign (Oct 16, 2024) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Peroxisome biogenesis disorder 2B	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002327634.4 First in ClinVar: Apr 08, 2022 Last updated: Feb 25, 2025	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs749232654 ...

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 Feb 26, 2025