NM_012388.4(BLOC1S6):c.461G>A (p.Arg154Gln) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 27, 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:: RCV004591659.2

Allele description [Variation Report for NM_012388.4(BLOC1S6):c.461G>A (p.Arg154Gln)]

NM_012388.4(BLOC1S6):c.461G>A (p.Arg154Gln)

Gene:

BLOC1S6:biogenesis of lysosomal organelles complex 1 subunit 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q21.1

Genomic location:

Preferred name:

NM_012388.4(BLOC1S6):c.461G>A (p.Arg154Gln)

Other names:

p.Arg154Gln

HGVS:

NC_000015.10:g.45606456G>A
NG_028194.2:g.24238G>A
NM_001311255.1:c.476G>A
NM_001311256.1:c.*112G>A
NM_012388.2:c.461G>A
NM_012388.4:c.461G>AMANE SELECT
NP_001298184.1:p.Arg159Gln
NP_036520.1:p.Arg154Gln
LRG_883:g.24238G>A
NC_000015.9:g.45898654G>A
NM_012388.3:c.461G>A
NR_132350.1:n.790G>A
NR_132351.2:n.522G>A
NR_132352.2:n.438G>A
NR_132353.1:n.640G>A
NR_132354.1:n.636G>A
NR_132355.2:n.296G>A
NR_132356.2:n.484G>A
NR_132357.2:n.397G>A
NR_132358.1:n.386G>A
NR_132359.2:n.254G>A

Protein change:

R154Q

Links:

dbSNP: rs145937442

NCBI 1000 Genomes Browser:

rs145937442

Molecular consequence:

NM_001311256.1:c.*112G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001311255.1:c.476G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_012388.4:c.461G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_132350.1:n.790G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132351.2:n.522G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132352.2:n.438G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132353.1:n.640G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132354.1:n.636G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132355.2:n.296G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132356.2:n.484G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132357.2:n.397G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132358.1:n.386G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132359.2:n.254G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005078950	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Apr 13, 2023)	germline	clinical testing	Citation Link,
SCV005409943	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 27, 2023)	germline	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

SCV005078950

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Apr 13, 2023)

germline

clinical testing

Citation Link,

SCV005409943

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 27, 2023)

germline

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	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 GeneDx, SCV005078950.1

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	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 Mayo Clinic Laboratories, Mayo Clinic, SCV005409943.1

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

Description

BP4

#	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		1	not provided	not provided	not provided

Last Updated: Nov 30, 2024

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