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NM_022081.6(HPS4):c.1873C>T (p.Gln625Ter) AND Hermansky-Pudlak syndrome 4

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 1, 2023
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:
RCV003469836.1

Allele description [Variation Report for NM_022081.6(HPS4):c.1873C>T (p.Gln625Ter)]

NM_022081.6(HPS4):c.1873C>T (p.Gln625Ter)

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.1873C>T (p.Gln625Ter)
HGVS:
  • NC_000022.11:g.26457941G>A
  • NG_009763.2:g.30923C>T
  • NM_001349896.1:c.1873C>T
  • NM_001349898.2:c.1873C>T
  • NM_001349899.2:c.1873C>T
  • NM_001349900.2:c.1927C>T
  • NM_001349901.1:c.1927C>T
  • NM_001349902.1:c.1714-4537C>T
  • NM_001349903.2:c.1714-4537C>T
  • NM_001349904.2:c.1873C>T
  • NM_001349905.1:c.1873C>T
  • NM_001410832.1:c.1873C>T
  • NM_022081.6:c.1873C>TMANE SELECT
  • NM_152841.2:c.1858C>T
  • NP_001336825.1:p.Gln625Ter
  • NP_001336827.1:p.Gln625Ter
  • NP_001336828.1:p.Gln625Ter
  • NP_001336829.1:p.Gln643Ter
  • NP_001336830.1:p.Gln643Ter
  • NP_001336833.1:p.Gln625Ter
  • NP_001336834.1:p.Gln625Ter
  • NP_001397761.1:p.Gln625Ter
  • NP_071364.4:p.Gln625Ter
  • NP_071364.4:p.Gln625Ter
  • NP_690054.1:p.Gln620Ter
  • LRG_590t1:c.1873C>T
  • LRG_590t2:c.1858C>T
  • LRG_590:g.30923C>T
  • LRG_590p1:p.Gln625Ter
  • LRG_590p2:p.Gln620Ter
  • NC_000022.10:g.26853907G>A
  • NM_022081.5:c.1873C>T
  • NR_073135.1:n.2559C>T
  • NR_073136.2:n.2128C>T
  • NR_146311.2:n.2570C>T
  • NR_146312.1:n.2475C>T
  • NR_146313.2:n.2415C>T
  • NR_146314.1:n.2626C>T
  • NR_146315.2:n.2486C>T
  • NR_146316.2:n.2461C>T
Protein change:
Q620*
Molecular consequence:
  • NM_001349902.1:c.1714-4537C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349903.2:c.1714-4537C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_073135.1:n.2559C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073136.2:n.2128C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146311.2:n.2570C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146312.1:n.2475C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146313.2:n.2415C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146314.1:n.2626C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146315.2:n.2486C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146316.2:n.2461C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001349896.1:c.1873C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349898.2:c.1873C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349899.2:c.1873C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349900.2:c.1927C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349901.1:c.1927C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349904.2:c.1873C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349905.1:c.1873C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001410832.1:c.1873C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_022081.6:c.1873C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_152841.2:c.1858C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Hermansky-Pudlak syndrome 4 (HPS4)
Identifiers:
MONDO: MONDO:0013556; MedGen: C3484357; Orphanet: 231500; Orphanet: 79430; OMIM: 614073

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004192351Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(May 1, 2023) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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 Baylor Genetics, SCV004192351.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 30, 2023