NM_004560.4(ROR2):c.769G>A (p.Glu257Lys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 6, 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:: RCV002543545.2

Allele description [Variation Report for NM_004560.4(ROR2):c.769G>A (p.Glu257Lys)]

NM_004560.4(ROR2):c.769G>A (p.Glu257Lys)

Gene:

ROR2:receptor tyrosine kinase like orphan receptor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q22.31

Genomic location:

Preferred name:

NM_004560.4(ROR2):c.769G>A (p.Glu257Lys)

HGVS:

NC_000009.12:g.91733290C>T
NG_008089.1:g.221873G>A
NM_001318204.2:c.769G>A
NM_004560.4:c.769G>AMANE SELECT
NP_001305133.1:p.Glu257Lys
NP_004551.2:p.Glu257Lys
NC_000009.11:g.94495572C>T
NM_004560.3:c.769G>A

Protein change:

E257K

Links:

dbSNP: rs543118807

NCBI 1000 Genomes Browser:

rs543118807

Molecular consequence:

NM_001318204.2:c.769G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004560.4:c.769G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV003030158	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 6, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 33937263, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003030158

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 6, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Heterozygous Recurrent Mutations Inducing Dysfunction of ROR2 Gene in Patients With Short Stature.

Gui B, Yu C, Li X, Zhao S, Zhao H, Yan Z, Cheng X, Lin J, Zheng H, Shao J, Zhao Z, Zhao L, Niu Y, Zhao Z, Wang H, Xie B, Wei X, Gui C, Li C, Chen S, Wang Y, Song Y, et al.

Front Cell Dev Biol. 2021;9:661747. doi: 10.3389/fcell.2021.661747.

PubMed [citation]

PMID:: 33937263
PMCID:: PMC8080376

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003030158.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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 ROR2 protein function. ClinVar contains an entry for this variant (Variation ID: 1012279). This missense change has been observed in individual(s) with short stature (PMID: 33937263). This variant is present in population databases (rs543118807, gnomAD 0.02%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 257 of the ROR2 protein (p.Glu257Lys).

#	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: Feb 28, 2024

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