NM_197968.4(ZMYM2):c.1765C>T (p.Arg589Ter) AND Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 1, 2023
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:: RCV002291294.4

Allele description [Variation Report for NM_197968.4(ZMYM2):c.1765C>T (p.Arg589Ter)]

NM_197968.4(ZMYM2):c.1765C>T (p.Arg589Ter)

Gene:

ZMYM2:zinc finger MYM-type containing 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q12.11

Genomic location:

Preferred name:

NM_197968.4(ZMYM2):c.1765C>T (p.Arg589Ter)

HGVS:

NC_000013.11:g.20027232C>T
NG_023348.2:g.73563C>T
NM_001190964.4:c.1765C>T
NM_001190965.4:c.1765C>T
NM_001353157.2:c.1765C>T
NM_001353159.2:c.1765C>T
NM_001353161.3:c.1570C>T
NM_001353162.3:c.1765C>T
NM_001353163.2:c.1504C>T
NM_001353164.2:c.1765C>T
NM_001353165.2:c.1765C>T
NM_003453.6:c.1765C>T
NM_197968.4:c.1765C>TMANE SELECT
NP_001177893.1:p.Arg589Ter
NP_001177894.1:p.Arg589Ter
NP_001340086.1:p.Arg589Ter
NP_001340088.1:p.Arg589Ter
NP_001340090.1:p.Arg524Ter
NP_001340091.1:p.Arg589Ter
NP_001340092.1:p.Arg502Ter
NP_001340093.1:p.Arg589Ter
NP_001340094.1:p.Arg589Ter
NP_003444.1:p.Arg589Ter
NP_932072.1:p.Arg589Ter
NC_000013.10:g.20601372C>T
NM_003453.4:c.1765C>T
NM_003453.5:c.1765C>T
NR_148365.2:n.1959C>T

Protein change:

R502*

Links:

dbSNP: rs1952668177

NCBI 1000 Genomes Browser:

rs1952668177

Molecular consequence:

NR_148365.2:n.1959C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001190964.4:c.1765C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001190965.4:c.1765C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353157.2:c.1765C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353159.2:c.1765C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353161.3:c.1570C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353162.3:c.1765C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353163.2:c.1504C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353164.2:c.1765C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353165.2:c.1765C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_003453.6:c.1765C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_197968.4:c.1765C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002583826	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 1, 2023)	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

SCV002583826

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Dec 1, 2023)

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	not provided	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 Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV002583826.2

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

Description

PVS1_Strong, PS4_Moderate, PM2

#	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: Feb 4, 2024

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