NM_012388.4(BLOC1S6):c.491dup (p.Leu164fs) AND Hermansky-Pudlak syndrome 9

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 2, 2021
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:: RCV001342343.5

Allele description [Variation Report for NM_012388.4(BLOC1S6):c.491dup (p.Leu164fs)]

NM_012388.4(BLOC1S6):c.491dup (p.Leu164fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

15q21.1

Genomic location:

Preferred name:

NM_012388.4(BLOC1S6):c.491dup (p.Leu164fs)

HGVS:

NC_000015.10:g.45606486dup
NG_028194.2:g.24268dup
NM_001311255.1:c.506dup
NM_001311256.1:c.*142dup
NM_012388.4:c.491dupMANE SELECT
NP_001298184.1:p.Leu169fs
NP_036520.1:p.Leu164fs
LRG_883:g.24268dup
NC_000015.9:g.45898682_45898683insT
NC_000015.9:g.45898684dup
NR_132350.1:n.820dup
NR_132351.2:n.552dup
NR_132352.2:n.468dup
NR_132353.1:n.670dup
NR_132354.1:n.666dup
NR_132355.2:n.326dup
NR_132356.2:n.514dup
NR_132357.2:n.427dup
NR_132358.1:n.416dup
NR_132359.2:n.284dup

Protein change:

L164fs

Links:

dbSNP: rs1350528661

NCBI 1000 Genomes Browser:

rs1350528661

Molecular consequence:

NM_001311256.1:c.*142dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001311255.1:c.506dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012388.4:c.491dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_132350.1:n.820dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132351.2:n.552dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132352.2:n.468dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132353.1:n.670dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132354.1:n.666dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132355.2:n.326dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132356.2:n.514dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132357.2:n.427dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132358.1:n.416dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_132359.2:n.284dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hermansky-Pudlak syndrome 9 (HPS9)
Identifiers:: MONDO: MONDO:0013606; MedGen: C3280026; Orphanet: 280663; Orphanet: 79430; OMIM: 614171

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001536270	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 2, 2021)	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

SCV001536270

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 2, 2021)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001536270.4

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

Description

This variant has not been reported in the literature in individuals with BLOC1S6-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change results in a frameshift in the BLOC1S6 gene (p.Leu164Phefs*33). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 9 amino acids of the BLOC1S6 protein and extend the protein by an additional 23 amino acids. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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