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NM_212550.5(BLOC1S3):c.338_341del (p.Leu113fs) AND Hermansky-Pudlak syndrome 8

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 30, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001257460.3

Allele description [Variation Report for NM_212550.5(BLOC1S3):c.338_341del (p.Leu113fs)]

NM_212550.5(BLOC1S3):c.338_341del (p.Leu113fs)

Gene:
BLOC1S3:biogenesis of lysosomal organelles complex 1 subunit 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19q13.32
Genomic location:
Preferred name:
NM_212550.5(BLOC1S3):c.338_341del (p.Leu113fs)
HGVS:
  • NC_000019.10:g.45179634_45179637del
  • NG_008372.1:g.5890_5893del
  • NG_033044.1:g.3610_3613del
  • NM_212550.5:c.338_341delMANE SELECT
  • NP_997715.1:p.Leu113fs
  • LRG_546:g.5890_5893del
  • NC_000019.9:g.45682892_45682895del
  • NM_212550.3:c.338_341del
Protein change:
L113fs
Links:
dbSNP: rs1568469902
NCBI 1000 Genomes Browser:
rs1568469902
Molecular consequence:
  • NM_212550.5:c.338_341del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Hermansky-Pudlak syndrome 8 (HPS8)
Identifiers:
MONDO: MONDO:0013560; MedGen: C3888026; Orphanet: 79430; OMIM: 614077

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001192839Laboratoire de Génétique Moléculaire, CHU Bordeaux
no assertion criteria provided
Pathogenic
(Mar 30, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Laboratoire de Génétique Moléculaire, CHU Bordeaux, SCV001192839.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testingnot provided

Description

This male patient was born to related parents from Brazil who both have brown hair and brown skin. He was referred to us for a suspicion of Hermansky-Pudlak syndrome. He was born with white hair and white skin and at age 10 he had blond hair, creamy skin and blue eyes with no pigmentation tendency. He had some pigmented and achromic naevi, and no history of skin cancer. He presented with congenital nystagmus, pupillary red reflection, photophobia, myopia, astigmatism and low visual acuity. Upon ophthalmological examination, retinal hypopigmentation was observed. Visual evoked potentials, electroretinography and optic coherence tomography could not be performed. His medical history is positive for bleeding diathesis but no signs of lung or digestive tract disease or immune defect were reported. NGS found a homozygous 4 bp frameshift deletion in the coding sequence of BLOC1S3, NM_212550.3: c.338_341del (p.(Leu113Argfs*15). This deletion is reported once, at heterozygous state, in the GnomAD database. ACMG Classification is in favor of a pathogenic variant (PVS1, PM2, PP1).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Apr 13, 2025