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NM_170675.5(MEIS2):c.992GAA[2] (p.Arg333del) AND Cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Nov 29, 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:
RCV000210625.7

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)

Name:
Cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
Synonyms:
CLEFT PALATE, CARDIAC DEFECTS, AND IMPAIRED INTELLECTUAL DEVELOPMENT
Identifiers:
MONDO: MONDO:0010970; MedGen: C1832950; OMIM: 600987

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000266813OMIM
no assertion criteria provided
Pathogenic
(Dec 19, 2022) 		germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV002760104Laboratory of Medical Genetics, University of Torino - NeuroWES
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Nov 29, 2022) 		germlineresearch

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

MEIS2 involvement in cardiac development, cleft palate, and intellectual disability.

Louw JJ, Corveleyn A, Jia Y, Hens G, Gewillig M, Devriendt K.

Am J Med Genet A. 2015 May;167A(5):1142-6. doi: 10.1002/ajmg.a.36989. Epub 2015 Feb 25.

PubMed [citation]
PMID:
25712757

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 OMIM, SCV000266813.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a 5-year-old girl with cleft palate, congenital heart defects, and moderate intellectual disability (CPCMR; 600987), Louw et al. (2015) identified a de novo heterozygous 3-bp in-frame deletion (c.998_1000del, NM_170674.2) in the MEIS2 gene, resulting in deletion of the highly conserved Arg333 residue in the homeodomain. The variant was found by exome sequencing and confirmed by Sanger sequencing. Functional studies and studies of patient cells were not performed, but the deletion was predicted to interfere with DNA binding and possibly to exert a dominant-negative effect rather than haploinsufficiency.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Medical Genetics, University of Torino - NeuroWES, SCV002760104.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024