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NM_022081.6(HPS4):c.1875G>T (p.Gln625His) AND Hermansky-Pudlak syndrome 4

Germline classification:
Benign (1 submission)
Last evaluated:
Aug 10, 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:
RCV001701683.2

Allele description [Variation Report for NM_022081.6(HPS4):c.1875G>T (p.Gln625His)]

NM_022081.6(HPS4):c.1875G>T (p.Gln625His)

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.1875G>T (p.Gln625His)
HGVS:
  • NC_000022.11:g.26457939C>A
  • NG_009763.2:g.30925G>T
  • NM_001349896.1:c.1875G>T
  • NM_001349898.2:c.1875G>T
  • NM_001349899.2:c.1875G>T
  • NM_001349900.2:c.1929G>T
  • NM_001349901.1:c.1929G>T
  • NM_001349902.1:c.1714-4535G>T
  • NM_001349903.2:c.1714-4535G>T
  • NM_001349904.2:c.1875G>T
  • NM_001349905.1:c.1875G>T
  • NM_022081.6:c.1875G>TMANE SELECT
  • NM_152841.2:c.1860G>T
  • NP_001336825.1:p.Gln625His
  • NP_001336827.1:p.Gln625His
  • NP_001336828.1:p.Gln625His
  • NP_001336829.1:p.Gln643His
  • NP_001336830.1:p.Gln643His
  • NP_001336833.1:p.Gln625His
  • NP_001336834.1:p.Gln625His
  • NP_071364.4:p.Gln625His
  • NP_071364.4:p.Gln625His
  • NP_690054.1:p.Gln620His
  • LRG_590t1:c.1875G>T
  • LRG_590t2:c.1860G>T
  • LRG_590:g.30925G>T
  • LRG_590p1:p.Gln625His
  • LRG_590p2:p.Gln620His
  • NC_000022.10:g.26853905C>A
  • NM_022081.4:c.1875G>T
  • NM_022081.5:c.1875G>T
  • NR_073135.1:n.2561G>T
  • NR_073136.2:n.2130G>T
  • NR_146311.2:n.2572G>T
  • NR_146312.1:n.2477G>T
  • NR_146313.2:n.2417G>T
  • NR_146314.1:n.2628G>T
  • NR_146315.2:n.2488G>T
  • NR_146316.2:n.2463G>T
  • Q9NQG7:p.Gln625His
Protein change:
Q620H
Links:
UniProtKB: Q9NQG7#VAR_021836; dbSNP: rs1894704
NCBI 1000 Genomes Browser:
rs1894704
Molecular consequence:
  • NM_001349902.1:c.1714-4535G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349903.2:c.1714-4535G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349896.1:c.1875G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349898.2:c.1875G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349899.2:c.1875G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349900.2:c.1929G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349901.1:c.1929G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349904.2:c.1875G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349905.1:c.1875G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022081.6:c.1875G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152841.2:c.1860G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_073135.1:n.2561G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073136.2:n.2130G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146311.2:n.2572G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146312.1:n.2477G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146313.2:n.2417G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146314.1:n.2628G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146315.2:n.2488G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146316.2:n.2463G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001933093Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)		Benign
(Aug 10, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot 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 Genome-Nilou Lab, SCV001933093.1

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

Last Updated: Sep 29, 2024