NC_000017.10:g.(?_3392509)_(3571820_?)del AND Spongy degeneration of central nervous system

Germline classification:: no classifications from unflagged records (1 submission)
Review status:: no classifications from unflagged records

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:: RCV003120773.5

Allele description [Variation Report for NC_000017.10:g.(?_3392509)_(3571820_?)del]

NC_000017.10:g.(?_3392509)_(3571820_?)del

Genes:

TAX1BP3:Tax1 binding protein 3 [Gene - OMIM - HGNC]
ASPA:aspartoacylase [Gene - OMIM - HGNC]
CTNS:cystinosin, lysosomal cystine transporter [Gene - OMIM - HGNC]
SHPK:sedoheptulokinase [Gene - OMIM - HGNC]
TRPV1:transient receptor potential cation channel subfamily V member 1 [Gene - OMIM - HGNC]
TRPV3:transient receptor potential cation channel subfamily V member 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p13.2

Genomic location:

Chr17: 3392509 - 3571820 (on Assembly GRCh37)

Preferred name:

NC_000017.10:g.(?_3392509)_(3571820_?)del

HGVS:

NC_000017.10:g.(?_3392509)_(3571820_?)del

Condition(s)

Name:: Spongy degeneration of central nervous system
Synonyms:: Canavan disease; Canavan-van Bogaert-Bertrand disease; Spongy degeneration of the central nervous system; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010079; MedGen: C0206307; Orphanet: 141; OMIM: 271900

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No clinical assertions found. See "Flagged submissions" below.

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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

The molecular basis of canavan (aspartoacylase deficiency) disease in European non-Jewish patients.

Shaag A, Anikster Y, Christensen E, Glustein JZ, Fois A, Michelakakis H, Nigro F, Pronicka E, Ribes A, Zabot MT, et al.

Am J Hum Genet. 1995 Sep;57(3):572-80.

PubMed [citation]

PMID:: 7668285
PMCID:: PMC1801272

Mutation detection in the aspartoacylase gene in 17 patients with Canavan disease: four new mutations in the non-Jewish population.

Sistermans EA, de Coo RF, van Beerendonk HM, Poll-The BT, Kleijer WJ, van Oost BA.

Eur J Hum Genet. 2000 Jul;8(7):557-60.

PubMed [citation]

PMID:: 10909858

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003790114.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 4-6 of the ASPA gene, which includes the termination codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to alter mRNA translation or result in a truncated protein product. This variant has not been reported in the literature in individuals affected with ASPA-related conditions. The region of the ASPA gene that includes exon(s) 4 has been determined to be clinically significant (PMID: 7668285, 10909858). Therefore, deletions that encompass that region are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003790114	Invitae	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003790114 appears to be redundant with SCV003793883. (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 28, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 7668285, 10909858, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003790114

Invitae

flagged submission

Reason: This record appears to be redundant with a more recent record from the same submitter.

Notes: SCV003790114 appears to be redundant with SCV003793883.

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 28, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Last Updated: Dec 9, 2023

ClinVar

Relating variation to medicine