NM_000308.4(CTSA):c.33GCT[7] (p.Leu19del) AND not provided

Germline classification:: Benign (4 submissions)
Last evaluated:: Jun 13, 2018
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:: RCV000588925.11

Allele description [Variation Report for NM_000308.4(CTSA):c.33GCT[7] (p.Leu19del)]

NM_000308.4(CTSA):c.33GCT[7] (p.Leu19del)

Gene:

CTSA:cathepsin A [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

20q13.12

Genomic location:

Preferred name:

NM_000308.4(CTSA):c.33GCT[7] (p.Leu19del)

HGVS:

NC_000020.10:g.44520238_44520240del
NC_000020.11:g.45891601GCT[7]
NG_008291.1:g.5650GCT[7]
NG_033108.1:g.4666CAG[7]
NM_000308.4:c.33GCT[7]MANE SELECT
NM_001127695.3:c.33GCT[7]
NM_001167594.3:c.33GCT[7]
NP_000299.3:p.Leu19del
NP_001121167.1:p.Leu19del
NP_001161066.2:p.Leu19del
NC_000020.10:g.44520238_44520240del
NC_000020.10:g.44520240GCT[7]
NC_000020.10:g.44520261_44520263delGCT
NM_000308.2:c.108_110delGCT
NM_000308.2:c.85_87delCTG
NM_000308.4:c.54_56delGCTMANE SELECT
NR_133656.2:n.78GCT[7]

Protein change:

L19del

Links:

dbSNP: rs72555383

NCBI 1000 Genomes Browser:

rs72555383

Molecular consequence:

NM_000308.4:c.33GCT[7] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001127695.3:c.33GCT[7] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001167594.3:c.33GCT[7] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_133656.2:n.78GCT[7] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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SRP133584 (429)
SRA
Nanorana cf. rarica SH-2019 voucher A2019_13 recombination activating protein 1 ...
Nanorana cf. rarica SH-2019 voucher A2019_13 recombination activating protein 1 (RAG1) gene, partial cds
gi|1799646101|gb|MN032608.1|

Nucleotide
recombination activating protein 1, partial [Nanorana sp. C SH-2019]
recombination activating protein 1, partial [Nanorana sp. C SH-2019]
gi|1799646074|gb|QHN69019.1|

Protein
Mus musculus FLYWCH family member 2 (Flywch2), transcript variant 1, mRNA
Mus musculus FLYWCH family member 2 (Flywch2), transcript variant 1, mRNA
gi|1268743694|ref|NM_029798.4|

Nucleotide
Nanorana 12S ribosomal RNA gene, partial sequence; mitochondrial.
Nanorana 12S ribosomal RNA gene, partial sequence; mitochondrial.
PopSet: 1799733903

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000801182	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Benign (Mar 15, 2017)	unknown	clinical testing
SCV000985844	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jun 13, 2018)	germline	clinical testing	Citation Link,
SCV001798606	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000801182

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Benign
(Mar 15, 2017)

unknown

clinical testing

SCV000985844

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Jun 13, 2018)

germline

clinical testing

Citation Link,

SCV001798606

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Likely benign

germline

clinical testing

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
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A case of galactosialidosis with novel mutations of the protective protein/cathepsin a gene: diagnosis prompted by trophoblast vacuolization on placental examination.

Kostadinov S, Shah BA, Alroy J, Phornphutkul C.

Pediatr Dev Pathol. 2014 Nov-Dec;17(6):474-7. doi: 10.2350/14-05-1500-CR.1. Epub 2014 Jul 30.

PubMed [citation]

PMID:: 25075748

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696509.1

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

Description

Variant summary: The CTSA c.108_110delGCT (p.Leu37del) variant involves the deletion of a luecine in a string of 9 leucines. One in silico tool predicts a polymorphism outcome for this variant. This variant was found in 144801/230752 control chromosomes (43432 homozygotes) at a frequency of 0.6275179, which is approximately 397 times the estimated maximal expected allele frequency of a pathogenic CTSA variant (0.0015811), suggesting this variant is likely a benign polymorphism. Taken together, this variant is classified as benign. One case report cites the variant in a GSL patient, along with two other variants that have not been reported by other clinical labs, therefore it is unclear which variants are disease-causing. Multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.

#	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

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801182.1

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

#	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 GeneDx, SCV000985844.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001798606.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	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
SCV000696509	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV000696509 appears to be redundant with SCV003928935. (LabCorp Variant Classification Summary - May 2015)	Benign (Nov 22, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000696509

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

flagged submission

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

Notes: SCV000696509 appears to be redundant with SCV003928935.

(LabCorp Variant Classification Summary - May 2015)

Benign
(Nov 22, 2017)

germline

clinical testing

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

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Last Updated: Apr 15, 2024

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