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NM_197968.4(ZMYM2):c.2434_2437del (p.Lys812fs) AND Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 14, 2021
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001667846.1

Allele description [Variation Report for NM_197968.4(ZMYM2):c.2434_2437del (p.Lys812fs)]

NM_197968.4(ZMYM2):c.2434_2437del (p.Lys812fs)

Gene:
ZMYM2:zinc finger MYM-type containing 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q12.11
Genomic location:
Preferred name:
NM_197968.4(ZMYM2):c.2434_2437del (p.Lys812fs)
HGVS:
  • NC_000013.11:g.20051574_20051577del
  • NG_023348.2:g.97905_97908del
  • NM_001190964.4:c.2434_2437del
  • NM_001190965.4:c.2434_2437del
  • NM_001353157.2:c.2434_2437del
  • NM_001353159.2:c.2434_2437del
  • NM_001353161.3:c.2239_2242del
  • NM_001353162.3:c.2434_2437del
  • NM_001353163.2:c.2173_2176del
  • NM_001353164.2:c.2434_2437del
  • NM_001353165.2:c.2434_2437del
  • NM_003453.6:c.2434_2437del
  • NM_197968.4:c.2434_2437delMANE SELECT
  • NP_001177893.1:p.Lys812fs
  • NP_001177894.1:p.Lys812fs
  • NP_001340086.1:p.Lys812fs
  • NP_001340088.1:p.Lys812fs
  • NP_001340090.1:p.Lys747fs
  • NP_001340091.1:p.Lys812fs
  • NP_001340092.1:p.Lys725fs
  • NP_001340093.1:p.Lys812fs
  • NP_001340094.1:p.Lys812fs
  • NP_003444.1:p.Lys812fs
  • NP_932072.1:p.Lys812fs
  • NC_000013.10:g.20625714_20625717del
  • NM_001190965.1:c.2434_2437delAAAG
  • NM_197968.2:c.2434_2437delAAAG
  • NR_148365.2:n.2628_2631del
Protein change:
K725fs
Links:
OMIM: 602221.0004; dbSNP: rs2140576563
NCBI 1000 Genomes Browser:
rs2140576563
Molecular consequence:
  • NM_001190964.4:c.2434_2437del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001190965.4:c.2434_2437del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353157.2:c.2434_2437del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353159.2:c.2434_2437del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353161.3:c.2239_2242del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353162.3:c.2434_2437del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353163.2:c.2173_2176del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353164.2:c.2434_2437del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353165.2:c.2434_2437del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003453.6:c.2434_2437del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_197968.4:c.2434_2437del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_148365.2:n.2628_2631del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities
Identifiers:
MONDO: MONDO:0859190; MedGen: C5561984; OMIM: 619522

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001890890OMIM
no assertion criteria provided
Pathogenic
(Sep 14, 2021) 		germlineliterature only

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

Help

Summary from all submissions

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

Citations

PubMed

Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations.

Connaughton DM, Dai R, Owen DJ, Marquez J, Mann N, Graham-Paquin AL, Nakayama M, Coyaud E, Laurent EMN, St-Germain JR, Blok LS, Vino A, Klämbt V, Deutsch K, Wu CW, Kolvenbach CM, Kause F, Ottlewski I, Schneider R, Kitzler TM, Majmundar AJ, Buerger F, et al.

Am J Hum Genet. 2020 Oct 1;107(4):727-742. doi: 10.1016/j.ajhg.2020.08.013. Epub 2020 Sep 4.

PubMed [citation]
PMID:
32891193
PMCID:
PMC7536580

Details of each submission

From OMIM, SCV001890890.1

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

Description

In 2 sibs (GM6-21 and GM6-22) with neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities (NECRC; 619522), Connaughton et al. (2020) identified a heterozygous 4-bp deletion (c.2434_2437delAAAG, NM_197968.2) in exon 13 of the ZMYM2 gene, resulting in a frameshift and premature termination (Lys812AspfsTer18). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD database. The mutation was predicted to result in nonsense-mediated mRNA decay, but studies of patient cells were not performed. Detailed in vitro cellular studies and animal models indicated that the mutation may cause a loss of function and haploinsufficiency, although a dominant-negative effect was also suggested. Both patients had normal renal ultrasounds. One had cardiac septal defects, microcephaly, and developmental delay, whereas the other only had speech delay.

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

Last Updated: Dec 24, 2023