NM_000069.3(CACNA1S):c.530C>T (p.Ser177Leu) AND not provided

Germline classification:: Uncertain significance (2 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:: RCV000996101.21

Allele description [Variation Report for NM_000069.3(CACNA1S):c.530C>T (p.Ser177Leu)]

NM_000069.3(CACNA1S):c.530C>T (p.Ser177Leu)

Gene:

CACNA1S:calcium voltage-gated channel subunit alpha1 S [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q32.1

Genomic location:

Preferred name:

NM_000069.3(CACNA1S):c.530C>T (p.Ser177Leu)

HGVS:

NC_000001.11:g.201091983G>A
NG_009816.2:g.25584C>T
NM_000069.3:c.530C>TMANE SELECT
NP_000060.2:p.Ser177Leu
NC_000001.10:g.201061111G>A
NG_009816.1:g.25584C>T
NM_000069.2:c.530C>T

Protein change:

S177L

Links:

dbSNP: rs141204958

NCBI 1000 Genomes Browser:

rs141204958

Molecular consequence:

NM_000069.3:c.530C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001150573	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Mar 1, 2024)	germline	clinical testing	Citation Link,
SCV003800441	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Uncertain significance (Nov 23, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001150573

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Uncertain significance
(Mar 1, 2024)

germline

clinical testing

Citation Link,

SCV003800441

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)

Uncertain significance
(Nov 23, 2022)

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
not provided	germline	yes	4	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001150573.21

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	not provided

Description

CACNA1S: PP3

#	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		4	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV003800441.2

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

Description

The CACNA1S c.530C>T; p.Ser177Leu variant (rs141204958), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 199686). This variant is found in the non-Finnish European population with an allele frequency of 0.08% (98/128994 alleles) in the Genome Aggregation Database. The serine at codon 177 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.897). While the high population frequency suggests that this is likely a benign variant, given the lack of clinical and functional data, the significance of the p.Ser177Leu variant is uncertain at this time.

#	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: Apr 15, 2024

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