VCV000157554.3 - ClinVar

NM_001370100.5(ZMYND11):c.561del (p.Met187fs)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001370100.5(ZMYND11):c.561del (p.Met187fs)

Variation ID: 157554 Accession: VCV000157554.3

Type and length

Deletion, 1 bp

Location

Cytogenetic: 10p15.3 10: 237629 (GRCh38) [ NCBI UCSC ] 10: 283569 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Nov 9, 2014	Sep 17, 2022	Oct 1, 2014

HGVS

Nucleotide	Protein	Molecular consequence
NM_001370100.5:c.561del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001357029.1:p.Met187fs	frameshift
NM_001202464.3:c.399del	NP_001189393.1:p.Met133fs	frameshift
NM_001202465.3:c.354+714del		intron variant
NM_001202466.3:c.399del	NP_001189395.1:p.Met133fs	frameshift
NM_001202467.1:c.399del	NP_001189396.1:p.Met133fs	frameshift
NM_001202468.1:c.561del	NP_001189397.1:p.Met187fs	frameshift
NM_001330057.3:c.510del	NP_001316986.1:p.Met170fs	frameshift
NM_001370097.3:c.561del	NP_001357026.1:p.Met187fs	frameshift
NM_001370098.2:c.561del	NP_001357027.1:p.Met187fs	frameshift
NM_001370099.2:c.561del	NP_001357028.1:p.Met187fs	frameshift
NM_001370101.2:c.561del	NP_001357030.1:p.Met187fs	frameshift
NM_001370102.2:c.561del	NP_001357031.1:p.Met187fs	frameshift
NM_001370103.2:c.399del	NP_001357032.1:p.Met133fs	frameshift
NM_001370104.2:c.399del	NP_001357033.1:p.Met133fs	frameshift
NM_001370105.2:c.399del	NP_001357034.1:p.Met133fs	frameshift
NM_001370106.2:c.399del	NP_001357035.1:p.Met133fs	frameshift
NM_001370107.2:c.399del	NP_001357036.1:p.Met133fs	frameshift
NM_001370108.2:c.399del	NP_001357037.1:p.Met133fs	frameshift
NM_001370109.2:c.399del	NP_001357038.1:p.Met133fs	frameshift
NM_001370110.2:c.354+714del		intron variant
NM_001370111.2:c.399del	NP_001357040.1:p.Met133fs	frameshift
NM_001370112.2:c.510del	NP_001357041.1:p.Met170fs	frameshift
NM_001370113.2:c.516+714del		intron variant
NM_001370114.2:c.516+714del		intron variant
NM_001370115.2:c.561del	NP_001357044.1:p.Met187fs	frameshift
NM_001370116.2:c.495del	NP_001357045.1:p.Met165fs	frameshift
NM_001370117.2:c.561del	NP_001357046.1:p.Met187fs	frameshift
NM_001370118.2:c.441del	NP_001357047.1:p.Met147fs	frameshift
NM_001370119.2:c.561del	NP_001357048.1:p.Met187fs	frameshift
NM_001370120.2:c.333del	NP_001357049.1:p.Met111fs	frameshift
NM_001370121.2:c.279del	NP_001357050.1:p.Met93fs	frameshift
NM_001370122.2:c.399del	NP_001357051.1:p.Met133fs	frameshift
NM_001370123.2:c.348del	NP_001357052.1:p.Met116fs	frameshift
NM_001370124.3:c.90del	NP_001357053.1:p.Met30fs	frameshift
NM_006624.7:c.561del	NP_006615.2:p.Met187fs	frameshift
NM_212479.4:c.561del	NP_997644.2:p.Met187fs	frameshift
NR_163254.2:n.648del		non-coding transcript variant
NC_000010.11:g.237629del
NC_000010.10:g.283569del
NG_029960.1:g.108165del

... more HGVS ... less HGVS

Protein change

M170fs, M30fs, M111fs, M165fs, M116fs, M133fs, M147fs, M187fs, M93fs

Other names

Canonical SPDI

NC_000010.11:237628:G:

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA170957 OMIM: 608668.0005 dbSNP: rs672601341 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
ZMYND11		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	226	362

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Intellectual disability, autosomal dominant 30	Pathogenic (1)	no assertion criteria provided	Oct 1, 2014	RCV000144899.5

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Oct 01, 2014)	no assertion criteria provided Method: literature only	INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 30, WITH SPEECH DELAY AND BEHAVIORAL ABNORMALITIES Affected status: not provided Allele origin: germline	OMIM Accession: SCV000191901.3 First in ClinVar: Nov 09, 2014 Last updated: Sep 17, 2022	Publications: PubMed (1) PubMed: 25217958 Comment on evidence: In a 25-year-old man (DNA-013587) with autosomal dominant intellectual developmental disorder-30 with speech delay and behavioral abnormalities (MRD30; 616083) and in his more mildly affected … (more) In a 25-year-old man (DNA-013587) with autosomal dominant intellectual developmental disorder-30 with speech delay and behavioral abnormalities (MRD30; 616083) and in his more mildly affected father, Coe et al. (2014) detected heterozygosity for a 1-bp deletion in the ZMYND11 gene (g.283569del) that resulted in a met187-to-ile substitution followed by frameshift and premature termination of the protein (Met187IlefsTer19). Functional studies of the variant were not performed. The proband had an IQ of 63 at age 9 years and 66 at age 18 years but of 55 at age 25 years. He had significant problems with low frustration tolerance and aggressive and provocative behavior, requiring treatment with risperidone. Dysmorphic features included synophrys, ptosis, and hypertelorism. The father of the proband had developmental delay but could read, write, calculate, and obtain a driving license. He had behavioral problems in childhood that included aggression and mood swings. (less)

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Refining analyses of copy number variation identifies specific genes associated with developmental delay.	Coe BP	Nature genetics	2014	PMID: 25217958

Text-mined citations for rs672601341 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 06, 2023

ClinVar Genomic variation as it relates to human health

NM_001370100.5(ZMYND11):c.561del (p.Met187fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs672601341 ...