NM_022081.6(HPS4):c.1415C>T (p.Pro472Leu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 20, 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:: RCV001963588.7

Allele description [Variation Report for NM_022081.6(HPS4):c.1415C>T (p.Pro472Leu)]

NM_022081.6(HPS4):c.1415C>T (p.Pro472Leu)

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.1415C>T (p.Pro472Leu)

HGVS:

NC_000022.11:g.26464215G>A
NG_009763.2:g.24649C>T
NM_001349896.1:c.1415C>T
NM_001349898.2:c.1415C>T
NM_001349899.2:c.1415C>T
NM_001349900.2:c.1469C>T
NM_001349901.1:c.1469C>T
NM_001349902.1:c.1415C>T
NM_001349903.2:c.1415C>T
NM_001349904.2:c.1415C>T
NM_001349905.1:c.1415C>T
NM_022081.6:c.1415C>TMANE SELECT
NM_152841.2:c.1400C>T
NP_001336825.1:p.Pro472Leu
NP_001336827.1:p.Pro472Leu
NP_001336828.1:p.Pro472Leu
NP_001336829.1:p.Pro490Leu
NP_001336830.1:p.Pro490Leu
NP_001336831.1:p.Pro472Leu
NP_001336832.1:p.Pro472Leu
NP_001336833.1:p.Pro472Leu
NP_001336834.1:p.Pro472Leu
NP_071364.4:p.Pro472Leu
NP_690054.1:p.Pro467Leu
LRG_590t2:c.1400C>T
LRG_590:g.24649C>T
LRG_590p2:p.Pro467Leu
NC_000022.10:g.26860181G>A
NR_073135.1:n.2101C>T
NR_073136.2:n.1670C>T
NR_146311.2:n.2112C>T
NR_146312.1:n.2017C>T
NR_146313.2:n.1957C>T
NR_146314.1:n.2168C>T
NR_146315.2:n.2028C>T
NR_146316.2:n.2003C>T

Protein change:

P467L

Links:

dbSNP: rs1411662887

NCBI 1000 Genomes Browser:

rs1411662887

Molecular consequence:

NM_001349896.1:c.1415C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001349898.2:c.1415C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001349899.2:c.1415C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001349900.2:c.1469C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001349901.1:c.1469C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001349902.1:c.1415C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001349903.2:c.1415C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001349904.2:c.1415C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001349905.1:c.1415C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_022081.6:c.1415C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_152841.2:c.1400C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_073135.1:n.2101C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_073136.2:n.1670C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146311.2:n.2112C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146312.1:n.2017C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146313.2:n.1957C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146314.1:n.2168C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146315.2:n.2028C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146316.2:n.2003C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002252739	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 20, 2021)	germline	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

SCV002252739

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 20, 2021)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002252739.4

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

Description

This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with leucine at codon 472 of the HPS4 protein (p.Pro472Leu). The proline residue is weakly conserved and there is a moderate physicochemical difference between proline and leucine. This variant has not been reported in the literature in individuals with HPS4-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0").

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

Last Updated: Sep 29, 2024

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