NM_197968.4(ZMYM2):c.1095del (p.His365fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 7, 2021
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:: RCV001900498.4

Allele description [Variation Report for NM_197968.4(ZMYM2):c.1095del (p.His365fs)]

NM_197968.4(ZMYM2):c.1095del (p.His365fs)

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.1095del (p.His365fs)

HGVS:

NC_000013.11:g.20003097del
NG_023348.2:g.49428del
NM_001190964.4:c.1095del
NM_001190965.4:c.1095del
NM_001353157.2:c.1095del
NM_001353159.2:c.1095del
NM_001353161.3:c.900del
NM_001353162.3:c.1095del
NM_001353163.2:c.834del
NM_001353164.2:c.1095del
NM_001353165.2:c.1095del
NM_003453.6:c.1095del
NM_197968.4:c.1095delMANE SELECT
NP_001177893.1:p.His365fs
NP_001177894.1:p.His365fs
NP_001340086.1:p.His365fs
NP_001340088.1:p.His365fs
NP_001340090.1:p.His300fs
NP_001340091.1:p.His365fs
NP_001340092.1:p.His278fs
NP_001340093.1:p.His365fs
NP_001340094.1:p.His365fs
NP_003444.1:p.His365fs
NP_932072.1:p.His365fs
NC_000013.10:g.20577237del
NC_000013.10:g.20577237delC
NR_148365.2:n.1289del

Protein change:

H278fs

Links:

dbSNP: rs2139912590

NCBI 1000 Genomes Browser:

rs2139912590

Molecular consequence:

NM_001190964.4:c.1095del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001190965.4:c.1095del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353157.2:c.1095del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353159.2:c.1095del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353161.3:c.900del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353162.3:c.1095del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353163.2:c.834del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353164.2:c.1095del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353165.2:c.1095del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003453.6:c.1095del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_197968.4:c.1095del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_148365.2:n.1289del - 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
SCV002138883	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 7, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 32891193, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002138883

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 7, 2021)

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

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

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002138883.3

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with ZMYM2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.His365Glnfs*16) in the ZMYM2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ZMYM2 are known to be pathogenic (PMID: 32891193).

#	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: Sep 29, 2024

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