NM_001122681.2(SH3BP2):c.1145C>G (p.Ala382Gly) AND Fibrous dysplasia of jaw

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 4, 2022
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:: RCV003620799.2

Allele description [Variation Report for NM_001122681.2(SH3BP2):c.1145C>G (p.Ala382Gly)]

NM_001122681.2(SH3BP2):c.1145C>G (p.Ala382Gly)

Gene:

SH3BP2:SH3 domain binding protein 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4p16.3

Genomic location:

Preferred name:

NM_001122681.2(SH3BP2):c.1145C>G (p.Ala382Gly)

HGVS:

NC_000004.12:g.2830051C>G
NG_011609.1:g.42029C>G
NM_001122681.2:c.1145C>GMANE SELECT
NM_001145855.2:c.1229C>G
NM_001145856.2:c.1316C>G
NM_003023.4:c.1145C>G
NP_001116153.1:p.Ala382Gly
NP_001139327.1:p.Ala410Gly
NP_001139328.1:p.Ala439Gly
NP_003014.3:p.Ala382Gly
LRG_1334t1:c.1145C>G
LRG_1334t2:c.1229C>G
LRG_1334:g.42029C>G
LRG_1334p1:p.Ala382Gly
LRG_1334p2:p.Ala410Gly
NC_000004.11:g.2831778C>G

Protein change:

A382G

Molecular consequence:

NM_001122681.2:c.1145C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001145855.2:c.1229C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001145856.2:c.1316C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003023.4:c.1145C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Fibrous dysplasia of jaw (CRBM)
Synonyms:: Cherubism
Identifiers:: MONDO: MONDO:0007315; MedGen: C0008029; Orphanet: 184; OMIM: 118400

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Metagenome or environmental sample from metagenome
Metagenome or environmental sample from metagenome

biosample
SAMN37230396 (1)
SRA
Dacelo leachi voucher UWBM60802 NADH dehydrogenase subunit 2 (ND2) gene, complet...
Dacelo leachi voucher UWBM60802 NADH dehydrogenase subunit 2 (ND2) gene, complete cds; mitochondrial
gi|74272481|gb|DQ111865.1|

Nucleotide
Melidora macrorrhina voucher AM897 NADH dehydrogenase subunit 2 (ND2) gene, comp...
Melidora macrorrhina voucher AM897 NADH dehydrogenase subunit 2 (ND2) gene, complete cds; mitochondrial
gi|74272483|gb|DQ111866.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004492016	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 4, 2022)	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

SCV004492016

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 4, 2022)

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, SCV004492016.1

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

Description

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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SH3BP2 protein function. This variant has not been reported in the literature in individuals affected with SH3BP2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 382 of the SH3BP2 protein (p.Ala382Gly).

#	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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