NM_170675.5(MEIS2):c.992GAA[2] (p.Arg333del) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Apr 21, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000494204.5

Allele description [Variation Report for NM_170675.5(MEIS2):c.992GAA[2] (p.Arg333del)]

NM_170675.5(MEIS2):c.992GAA[2] (p.Arg333del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

15q14

Genomic location:

Preferred name:

NM_170675.5(MEIS2):c.992GAA[2] (p.Arg333del)

HGVS:

NC_000015.10:g.36896665TCT[2]
NG_029108.1:g.209628GAA[2]
NM_001220482.2:c.992GAA[2]
NM_002399.4:c.953GAA[2]
NM_170674.5:c.992GAA[2]
NM_170675.5:c.992GAA[2]MANE SELECT
NM_170676.5:c.992GAA[2]
NM_170677.5:c.992GAA[2]
NM_172315.3:c.953GAA[2]
NM_172316.3:c.728GAA[2]
NP_001207411.1:p.Arg333del
NP_002390.1:p.Arg320del
NP_733774.1:p.Arg333del
NP_733775.1:p.Arg333del
NP_733776.1:p.Arg333del
NP_733777.1:p.Arg333del
NP_758526.1:p.Arg320del
NP_758527.1:p.Arg245del
NC_000015.9:g.37188866TCT[2]
NM_170674.2:c.998_1000del
NM_170674.4:c.998_1000del
NM_170674.4:c.998_1000delGAA
NM_170675.3:c.998_1000delGAA
NM_170675.5:c.998_1000delMANE SELECT
NM_170677.4:c.998_1000delGAA
NR_051953.2:n.1998GAA[2]

Protein change:

R245del

Links:

OMIM: 601740.0001; dbSNP: rs879255264

NCBI 1000 Genomes Browser:

rs879255264

Molecular consequence:

NM_001220482.2:c.992GAA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_002399.4:c.953GAA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_170674.5:c.992GAA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_170675.5:c.992GAA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_170676.5:c.992GAA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_170677.5:c.992GAA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_172315.3:c.953GAA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_172316.3:c.728GAA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_051953.2:n.1998GAA[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000582364	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 21, 2023)	germline	clinical testing	Citation Link,
SCV001447369	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 23, 2020)	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

SCV000582364

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 21, 2023)

germline

clinical testing

Citation Link,

SCV001447369

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 23, 2020)

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	yes	not provided	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000582364.5

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25712757, 30055086, 33091211, 34217350)

#	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

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001447369.1

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

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

Last Updated: Jun 23, 2024

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