NM_170675.5(MEIS2):c.905C>T (p.Pro302Leu) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 3, 2017
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:: RCV000482887.2

Allele description [Variation Report for NM_170675.5(MEIS2):c.905C>T (p.Pro302Leu)]

NM_170675.5(MEIS2):c.905C>T (p.Pro302Leu)

Gene:

MEIS2:Meis homeobox 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q14

Genomic location:

Preferred name:

NM_170675.5(MEIS2):c.905C>T (p.Pro302Leu)

HGVS:

NC_000015.10:g.36950396G>A
NG_029108.1:g.155904C>T
NG_053466.1:g.1893G>A
NM_001220482.2:c.905C>T
NM_002399.4:c.866C>T
NM_170674.5:c.905C>T
NM_170675.5:c.905C>TMANE SELECT
NM_170676.5:c.905C>T
NM_170677.5:c.905C>T
NM_172315.3:c.866C>T
NM_172316.3:c.641C>T
NP_001207411.1:p.Pro302Leu
NP_002390.1:p.Pro289Leu
NP_733774.1:p.Pro302Leu
NP_733775.1:p.Pro302Leu
NP_733776.1:p.Pro302Leu
NP_733777.1:p.Pro302Leu
NP_758526.1:p.Pro289Leu
NP_758527.1:p.Pro214Leu
NC_000015.9:g.37242597G>A
NM_170674.4:c.905C>T
NM_170677.4:c.905C>T

Protein change:

P214L; PRO302LEU

Links:

OMIM: 601740.0004; dbSNP: rs1064793383

NCBI 1000 Genomes Browser:

rs1064793383

Molecular consequence:

NM_001220482.2:c.905C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002399.4:c.866C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_170674.5:c.905C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_170675.5:c.905C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_170676.5:c.905C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_170677.5:c.905C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_172315.3:c.866C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_172316.3:c.641C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000565972	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Aug 3, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000565972

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Aug 3, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000565972.3

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

Description

The P302L variant in the MEIS2 gene has not been published as a pathogenic variant nor has it been reported as a benign polymorphism to our knowledge. The P302L variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The P302L variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is highly conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. The P302L variant is a good candidate for a disease-causing variant; however, the possibility it may be a rare benign variant cannot be excluded.

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

Last Updated: Aug 5, 2023

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