NM_000049.4(ASPA):c.382del (p.Glu129fs) AND Spongy degeneration of central nervous system

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Dec 11, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000667104.11

Allele description [Variation Report for NM_000049.4(ASPA):c.382del (p.Glu129fs)]

NM_000049.4(ASPA):c.382del (p.Glu129fs)

Genes:

ASPA:aspartoacylase [Gene - OMIM - HGNC]
SPATA22:spermatogenesis associated 22 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_000049.4(ASPA):c.382del (p.Glu129fs)

HGVS:

NC_000017.11:g.3481748del
NG_008399.2:g.13103del
NG_008399.3:g.12640del
NM_000049.4:c.382delMANE SELECT
NM_001128085.1:c.382del
NM_001321336.2:c.-73-12350del
NM_001321337.2:c.-73-12350del
NP_000040.1:p.Glu129fs
NP_001121557.1:p.Glu129fs
NC_000017.10:g.3385042del
NM_000049.2:c.382delC

Protein change:

E129fs

Links:

dbSNP: rs1555538825

NCBI 1000 Genomes Browser:

rs1555538825

Molecular consequence:

NM_000049.4:c.382del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001128085.1:c.382del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001321336.2:c.-73-12350del - intron variant - [Sequence Ontology: SO:0001627]
NM_001321337.2:c.-73-12350del - intron variant - [Sequence Ontology: SO:0001627]

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

Recent activity

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Rbp1 retinol binding protein 1 [Rattus norvegicus]
Rbp1 retinol binding protein 1 [Rattus norvegicus]
Gene ID:25056

Gene
25056[uid] AND (alive[prop]) (1)
Gene
Mus musculus histidine triad nucleotide binding protein 3, mRNA (cDNA clone MGC:...
Mus musculus histidine triad nucleotide binding protein 3, mRNA (cDNA clone MGC:35712 IMAGE:4035971), complete cds
gi|19263852|gb|BC025065.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000791502	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (May 17, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV005052847	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 11, 2023)	unknown	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

SCV000791502

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(May 17, 2017)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV005052847

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 11, 2023)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Rapid detection of three large novel deletions of the aspartoacylase gene in non-Jewish patients with Canavan disease.

Zeng BJ, Wang ZH, Torres PA, Pastores GM, Leone P, Raghavan SS, Kolodny EH.

Mol Genet Metab. 2006 Sep-Oct;89(1-2):156-63. Epub 2006 Jul 18.

PubMed [citation]

PMID:: 16854607

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 Counsyl, SCV000791502.1

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

From Baylor Genetics, SCV005052847.1

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

Last Updated: Nov 3, 2024

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