NM_000308.4(CTSA):c.54G>C (p.Leu18=) AND not provided

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Mar 1, 2024
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:: RCV000675493.19

Allele description [Variation Report for NM_000308.4(CTSA):c.54G>C (p.Leu18=)]

NM_000308.4(CTSA):c.54G>C (p.Leu18=)

Genes:

LOC130065974:ATAC-STARR-seq lymphoblastoid active region 17954 [Gene]
CTSA:cathepsin A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q13.12

Genomic location:

Preferred name:

NM_000308.4(CTSA):c.54G>C (p.Leu18=)

HGVS:

NC_000020.11:g.45891622G>C
NG_008291.1:g.5671G>C
NG_033108.1:g.4666C>G
NM_000308.4:c.54G>CMANE SELECT
NM_001127695.3:c.54G>C
NM_001167594.3:c.54G>C
NP_000299.2:p.Leu36=
NP_000299.3:p.Leu18=
NP_001121167.1:p.Leu18=
NP_001161066.2:p.Leu18=
NC_000020.10:g.44520261G>C
NM_000308.2:c.108G>C
NM_000308.3:c.108G>C
NR_133656.2:n.99G>C

Links:

dbSNP: rs181943893

NCBI 1000 Genomes Browser:

rs181943893

Molecular consequence:

NR_133656.2:n.99G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000308.4:c.54G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127695.3:c.54G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001167594.3:c.54G>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000801183	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Likely benign (Dec 15, 2015)	unknown	clinical testing
SCV001750949	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Sep 8, 2020)	germline	clinical testing	Citation Link,
SCV004154609	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Mar 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000801183

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Likely benign
(Dec 15, 2015)

unknown

clinical testing

SCV001750949

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Sep 8, 2020)

germline

clinical testing

Citation Link,

SCV004154609

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Mar 1, 2024)

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	yes	3	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801183.1

#	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, SCV001750949.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV004154609.10

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

Description

CTSA: BP4, BP7

#	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		3	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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