NM_000308.4(CTSA):c.33GCT[9] (p.Leu19dup) AND not specified

Germline classification:: Benign (1 submission)
Last evaluated:: Jun 15, 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:: RCV000780204.2

Allele description [Variation Report for NM_000308.4(CTSA):c.33GCT[9] (p.Leu19dup)]

NM_000308.4(CTSA):c.33GCT[9] (p.Leu19dup)

Gene:

CTSA:cathepsin A [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

20q13.12

Genomic location:

Preferred name:

NM_000308.4(CTSA):c.33GCT[9] (p.Leu19dup)

HGVS:

NC_000020.11:g.45891601GCT[9]
NG_008291.1:g.5650GCT[9]
NG_033108.1:g.4666CAG[9]
NM_000308.3:c.108_110dupGCT
NM_000308.4:c.33GCT[9]MANE SELECT
NM_001127695.3:c.33GCT[9]
NM_001167594.3:c.33GCT[9]
NP_000299.3:p.Leu19dup
NP_001121167.1:p.Leu19dup
NP_001161066.2:p.Leu19dup
NC_000020.10:g.44520237_44520238insCTG
NC_000020.10:g.44520240GCT[9]
NM_000308.2:c.108_110dupGCT
NM_000308.3:c.108_110dup
NR_133656.2:n.78GCT[9]

Links:

dbSNP: rs72555383

NCBI 1000 Genomes Browser:

rs72555383

Molecular consequence:

NM_000308.4:c.33GCT[9] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001127695.3:c.33GCT[9] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001167594.3:c.33GCT[9] - inframe_insertion - [Sequence Ontology: SO:0001821]
NR_133656.2:n.78GCT[9] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000917270	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jun 15, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000917270

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Jun 15, 2018)

germline

clinical testing

Citation Link

Help

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000917270.1

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

Description

Variant summary: CTSA c.108_110dupGCT (p.Leu37dup) results in an in-frame insertion of a leucine into a repetitive region of the encoded protein sequence; this region consists of several consecutive leucines and doesn't have a known function. The variant allele was found at a frequency of 0.0055 in 230752 control chromosomes in the gnomAD database, including 5 homozygotes. The observed variant frequency is approximately 3.46 fold of the estimated maximal expected allele frequency for a pathogenic variant in CTSA causing Galactosialidosis phenotype (0.0016), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.108_110dupGCT in individuals affected with Galactosialidosis and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was 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

Last Updated: Oct 13, 2024

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