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NM_022081.6(HPS4):c.1899C>T (p.Val633=) AND Hermansky-Pudlak syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jun 14, 2016
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:
RCV000295465.5

Allele description [Variation Report for NM_022081.6(HPS4):c.1899C>T (p.Val633=)]

NM_022081.6(HPS4):c.1899C>T (p.Val633=)

Gene:
HPS4:HPS4 biogenesis of lysosomal organelles complex 3 subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q12.1
Genomic location:
Preferred name:
NM_022081.6(HPS4):c.1899C>T (p.Val633=)
HGVS:
  • NC_000022.11:g.26457915G>A
  • NG_009763.2:g.30949C>T
  • NM_001349896.1:c.1899C>T
  • NM_001349898.2:c.1899C>T
  • NM_001349899.2:c.1899C>T
  • NM_001349900.2:c.1953C>T
  • NM_001349901.1:c.1953C>T
  • NM_001349902.1:c.1714-4511C>T
  • NM_001349903.2:c.1714-4511C>T
  • NM_001349904.2:c.1899C>T
  • NM_001349905.1:c.1899C>T
  • NM_022081.6:c.1899C>TMANE SELECT
  • NM_152841.2:c.1884C>T
  • NP_001336825.1:p.Val633=
  • NP_001336827.1:p.Val633=
  • NP_001336828.1:p.Val633=
  • NP_001336829.1:p.Val651=
  • NP_001336830.1:p.Val651=
  • NP_001336833.1:p.Val633=
  • NP_001336834.1:p.Val633=
  • NP_071364.4:p.Val633=
  • NP_071364.4:p.Val633=
  • NP_690054.1:p.Val628=
  • LRG_590t1:c.1899C>T
  • LRG_590t2:c.1884C>T
  • LRG_590:g.30949C>T
  • LRG_590p1:p.Val633=
  • LRG_590p2:p.Val628=
  • NC_000022.10:g.26853881G>A
  • NM_022081.4:c.1899C>T
  • NM_022081.5:c.1899C>T
  • NR_073135.1:n.2585C>T
  • NR_073136.2:n.2154C>T
  • NR_146311.2:n.2596C>T
  • NR_146312.1:n.2501C>T
  • NR_146313.2:n.2441C>T
  • NR_146314.1:n.2652C>T
  • NR_146315.2:n.2512C>T
  • NR_146316.2:n.2487C>T
  • p.Val633Val
Links:
dbSNP: rs35993959
NCBI 1000 Genomes Browser:
rs35993959
Molecular consequence:
  • NM_001349902.1:c.1714-4511C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349903.2:c.1714-4511C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_073135.1:n.2585C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073136.2:n.2154C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146311.2:n.2596C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146312.1:n.2501C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146313.2:n.2441C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146314.1:n.2652C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146315.2:n.2512C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146316.2:n.2487C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001349896.1:c.1899C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001349898.2:c.1899C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001349899.2:c.1899C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001349900.2:c.1953C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001349901.1:c.1953C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001349904.2:c.1899C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001349905.1:c.1899C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_022081.6:c.1899C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_152841.2:c.1884C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hermansky-Pudlak syndrome (HPS)
Synonyms:
Albinism with hemorrhagic diathesis and pigmented reticuloendothelial cells
Identifiers:
MONDO: MONDO:0019312; MedGen: C0079504; OMIM: PS203300

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000437639Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification 20161018)		Likely benign
(Jun 14, 2016) 		germlineclinical testing

ICSL_Variant_Classification_20161018.pdf

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000437639.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024