VCV000030353.1 - ClinVar

NM_004813.4(PEX16):c.952+118_*82del

Germline

Classification

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.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_004813.4(PEX16):c.952+118_*82del

Variation ID: 30353 Accession: VCV000030353.1

Type and length

Deletion, 609 bp

Location

Cytogenetic: 11p11.2 11: 45910172-45910780 (GRCh38) [ NCBI UCSC ] 11: 45931723-45932331 (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 4, 2013	Apr 4, 2013	Sep 1, 2010

HGVS

Nucleotide	Protein	Molecular consequence
NM_004813.4:c.952+118_*82del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice acceptor
NM_057174.3:c.952+118_958del		splice acceptor
NC_000011.10:g.45910173_45910781del
NC_000011.9:g.45931724_45932332del
NG_008460.1:g.12344_12952del
NG_008460.2:g.13041_13649del
NG_008460.2:g.13042_13650del

... more HGVS ... less HGVS

Protein change

Other names

DEL, EX11

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

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

OMIM: 603360.0005 VarSome

Comment on variant

NCBI staff provided HGVS expressions for OMIM allelic variant 603360.0005 from this description in the paper by Ebberink et al., 2010 (PubMed 20647552): "intragenic deletion in transcription variant 1 comprising the last 468 base pairs of intron 10, the entire exon 11a and the first 80 base pairs of the 39 flanking region of exon 11a and in transcription variant 2 comprising the last 603 base pairs of intron 10, and the first 4 base pairs of exon 11b".

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.
PEX16		-	-	GRCh38 GRCh37	595	613

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 8B	Pathogenic (1)	no assertion criteria provided	Sep 1, 2010	RCV000023297.2

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.	More information 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.
Pathogenic (Sep 01, 2010)	no assertion criteria provided Method: literature only	PEROXISOME BIOGENESIS DISORDER 8B Affected status: not provided Allele origin: germline	OMIM Accession: SCV000044588.1 First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013	Publications: PubMed (1) PubMed: 20647552 Comment on evidence: In an Indian girl, born of consanguineous parents, with a relatively mild type of peroxisomal biogenesis disorder (PBD8B; 614877), Ebberink et al. (2010) identified a … (more) In an Indian girl, born of consanguineous parents, with a relatively mild type of peroxisomal biogenesis disorder (PBD8B; 614877), Ebberink et al. (2010) identified a homozygous large intragenic deletion of intron 10 and exon 11 of the PEX16 gene. In transcript variant 1, the deletion affected the last 468 base pairs of intron 10, the entire exon 11a, and the first 80 base pairs of the 3-prime flanking region of exon 11a. In transcript variant 2, the deletion affected the last 603 base pairs of intron 10, and the first 4 base pairs of exon 11b. The deletion resulted in 3 alternative splice products. She showed normal development for the first year of life, but then stopped acquiring new skills, and lost her ability to walk independently at age 24 months due to spasticity and mild ataxia. Her speech and other cognitive functions also deteriorated slowly over time. At the age of 5 years, she had nystagmus, cataracts, hyperreflexia, clonus, and extensor plantar responses. Brain imaging showed diffuse white matter abnormalities and focal atrophy of the cerebellum and corpus callosum. Peripheral nerve velocity studies of the lower limbs suggested demyelination. Studies of skin fibroblasts showed that the peroxisomes were markedly enlarged in size and reduced in number compared to controls. However, biochemical studies showed only mild abnormalities, such as increased VLCFA, but most other peroxisomal functions appeared normal. (less)

Germline Functional Evidence

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 germline classification of this variant

Title	Author	Journal	Year	Link
Identification of an unusual variant peroxisome biogenesis disorder caused by mutations in the PEX16 gene.	Ebberink MS	Journal of medical genetics	2010	PMID: 20647552

Text-mined citations for this variant ...

Record last updated Nov 03, 2024

ClinVar Genomic variation as it relates to human health

NM_004813.4(PEX16):c.952+118_*82del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...