NM_001122681.2(SH3BP2):c.17del (p.Met6fs) AND Fibrous dysplasia of jaw

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 19, 2024
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:: RCV000814840.7

Allele description [Variation Report for NM_001122681.2(SH3BP2):c.17del (p.Met6fs)]

NM_001122681.2(SH3BP2):c.17del (p.Met6fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

4p16.3

Genomic location:

Preferred name:

NM_001122681.2(SH3BP2):c.17del (p.Met6fs)

HGVS:

NC_000004.12:g.2820634del
NG_011609.1:g.32612del
NM_001122681.2:c.17delMANE SELECT
NM_001145855.2:c.101del
NM_001145856.2:c.188del
NM_003023.4:c.17del
NP_001116153.1:p.Met6fs
NP_001139327.1:p.Met34fs
NP_001139328.1:p.Met63fs
NP_003014.3:p.Met6fs
LRG_1334t1:c.17del
LRG_1334t2:c.101del
LRG_1334:g.32612del
LRG_1334p1:p.Met6fs
LRG_1334p2:p.Met34fs
NC_000004.11:g.2822361del
NC_000004.11:g.2822361delT
NM_003023.4:c.17delT

Protein change:

M34fs

Links:

dbSNP: rs746804160

NCBI 1000 Genomes Browser:

rs746804160

Molecular consequence:

NM_001122681.2:c.17del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001145855.2:c.101del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001145856.2:c.188del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003023.4:c.17del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000955268	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 19, 2024)	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

SCV000955268

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 19, 2024)

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, SCV000955268.6

#	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 creates a premature translational stop signal (p.Met6Serfs*7) in the SH3BP2 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in SH3BP2 cause disease. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SH3BP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 658097). 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

ClinVar

Relating variation to medicine