NM_022081.6(HPS4):c.1409T>G (p.Leu470Ter) AND Hermansky-Pudlak syndrome 4

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 25, 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:: RCV003461730.1

Allele description [Variation Report for NM_022081.6(HPS4):c.1409T>G (p.Leu470Ter)]

NM_022081.6(HPS4):c.1409T>G (p.Leu470Ter)

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.1409T>G (p.Leu470Ter)

HGVS:

NC_000022.11:g.26464221A>C
NG_009763.2:g.24643T>G
NM_001349896.1:c.1409T>G
NM_001349898.2:c.1409T>G
NM_001349899.2:c.1409T>G
NM_001349900.2:c.1463T>G
NM_001349901.1:c.1463T>G
NM_001349902.1:c.1409T>G
NM_001349903.2:c.1409T>G
NM_001349904.2:c.1409T>G
NM_001349905.1:c.1409T>G
NM_001410832.1:c.1409T>G
NM_022081.6:c.1409T>GMANE SELECT
NM_152841.2:c.1394T>G
NP_001336825.1:p.Leu470Ter
NP_001336827.1:p.Leu470Ter
NP_001336828.1:p.Leu470Ter
NP_001336829.1:p.Leu488Ter
NP_001336830.1:p.Leu488Ter
NP_001336831.1:p.Leu470Ter
NP_001336832.1:p.Leu470Ter
NP_001336833.1:p.Leu470Ter
NP_001336834.1:p.Leu470Ter
NP_001397761.1:p.Leu470Ter
NP_071364.4:p.Leu470Ter
NP_071364.4:p.Leu470Ter
NP_690054.1:p.Leu465Ter
LRG_590t1:c.1409T>G
LRG_590t2:c.1394T>G
LRG_590:g.24643T>G
LRG_590p1:p.Leu470Ter
LRG_590p2:p.Leu465Ter
NC_000022.10:g.26860187A>C
NM_022081.5:c.1409T>G
NR_073135.1:n.2095T>G
NR_073136.2:n.1664T>G
NR_146311.2:n.2106T>G
NR_146312.1:n.2011T>G
NR_146313.2:n.1951T>G
NR_146314.1:n.2162T>G
NR_146315.2:n.2022T>G
NR_146316.2:n.1997T>G

Protein change:

L465*

Molecular consequence:

NR_073135.1:n.2095T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_073136.2:n.1664T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146311.2:n.2106T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146312.1:n.2011T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146313.2:n.1951T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146314.1:n.2162T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146315.2:n.2022T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146316.2:n.1997T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001349896.1:c.1409T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001349898.2:c.1409T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001349899.2:c.1409T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001349900.2:c.1463T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001349901.1:c.1463T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001349902.1:c.1409T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001349903.2:c.1409T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001349904.2:c.1409T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001349905.1:c.1409T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001410832.1:c.1409T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_022081.6:c.1409T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_152841.2:c.1394T>G - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004192332	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 25, 2023)	unknown	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

SCV004192332

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 25, 2023)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV004192332.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 30, 2023

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