NM_003664.5(AP3B1):c.2779G>A (p.Gly927Ser) AND Hermansky-Pudlak syndrome 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 24, 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:: RCV000704289.6

Allele description [Variation Report for NM_003664.5(AP3B1):c.2779G>A (p.Gly927Ser)]

NM_003664.5(AP3B1):c.2779G>A (p.Gly927Ser)

Gene:

AP3B1:adaptor related protein complex 3 subunit beta 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q14.1

Genomic location:

Preferred name:

NM_003664.5(AP3B1):c.2779G>A (p.Gly927Ser)

HGVS:

NC_000005.10:g.78039073C>T
NG_007268.1:g.260632G>A
NM_001271769.2:c.2632G>A
NM_003664.3:c.2779G>A
NM_003664.5:c.2779G>AMANE SELECT
NP_001258698.1:p.Gly878Ser
NP_003655.3:p.Gly927Ser
NP_003655.3:p.Gly927Ser
LRG_170t1:c.2779G>A
LRG_170:g.260632G>A
LRG_170p1:p.Gly927Ser
NC_000005.9:g.77334897C>T
NM_003664.4:c.2779G>A

Protein change:

G878S

Links:

dbSNP: rs746205404

NCBI 1000 Genomes Browser:

rs746205404

Molecular consequence:

NM_001271769.2:c.2632G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003664.5:c.2779G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hermansky-Pudlak syndrome 2 (HPS2)
Synonyms:: Platelet defects and oculocutaneous albinism
Identifiers:: MONDO: MONDO:0011997; MedGen: C1842362; Orphanet: 79430; OMIM: 608233

Recent activity

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Swartzia langsdorffii voucher Iseppon s.n. (NY) authority Swartzia langsdorffii ...
Swartzia langsdorffii voucher Iseppon s.n. (NY) authority Swartzia langsdorffii Raddi trnL-trnF intergenic spacer, partial sequence; chloroplast
gi|155008109|gb|EF527528.1|

Nucleotide
UNVERIFIED: Uncultured bacterium clone OMZ_P1_137 16S ribosomal RNA-like gene, p...
UNVERIFIED: Uncultured bacterium clone OMZ_P1_137 16S ribosomal RNA-like gene, partial sequence
gi|1336620948|gb|MG860844.1|

Nucleotide
Albizia kalkora voucher Ge130807 5.8S ribosomal RNA gene, partial sequence; inte...
Albizia kalkora voucher Ge130807 5.8S ribosomal RNA gene, partial sequence; internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
gi|1439131449|gb|MH703081.1|

Nucleotide
Component(Core) Links for Nucleotide (Select 1519244473) (4)
Nucleotide
Bacillus sp. SRB_336 SRB_336_contig_14, whole genome shotgun sequence
Bacillus sp. SRB_336 SRB_336_contig_14, whole genome shotgun sequence
gi|1408825676|gb|NADW01000013.1||gn :NADW01|SRB_336_contig_14

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000833232	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 24, 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

SCV000833232

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 24, 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, SCV000833232.3

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

Description

This sequence change replaces glycine with serine at codon 927 of the AP3B1 protein (p.Gly927Ser). The glycine residue is moderately conserved and there is a small physicochemical difference between glycine and serine. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals affected with AP3B1-related conditions. 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"). 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.

#	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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