VCV000431092.1 - ClinVar

NM_001370100.5(ZMYND11):c.383del (p.Ser128fs)

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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001370100.5(ZMYND11):c.383del (p.Ser128fs)

Variation ID: 431092 Accession: VCV000431092.1

Type and length

Deletion, 1 bp

Location

Cytogenetic: 10p15.3 10: 221301 (GRCh38) [ NCBI UCSC ] 10: 267241 (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	Aug 5, 2017	Aug 5, 2017	Aug 1, 2017

HGVS

Nucleotide	Protein	Molecular consequence
NM_001370100.5:c.383del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001357029.1:p.Ser128fs	frameshift
NM_001202464.3:c.276+11253del		intron variant
NM_001202465.3:c.276+11253del		intron variant
NM_001202466.3:c.276+11253del		intron variant
NM_001202467.1:c.276+11253del		intron variant
NM_001202468.1:c.383del	NP_001189397.1:p.Ser128fs	frameshift
NM_001330057.3:c.332del	NP_001316986.1:p.Ser111fs	frameshift
NM_001370097.3:c.383del	NP_001357026.1:p.Ser128fs	frameshift
NM_001370098.2:c.383del	NP_001357027.1:p.Ser128fs	frameshift
NM_001370099.2:c.383del	NP_001357028.1:p.Ser128fs	frameshift
NM_001370101.2:c.383del	NP_001357030.1:p.Ser128fs	frameshift
NM_001370102.2:c.383del	NP_001357031.1:p.Ser128fs	frameshift
NM_001370103.2:c.276+11253del		intron variant
NM_001370104.2:c.276+11253del		intron variant
NM_001370105.2:c.276+11253del		intron variant
NM_001370106.2:c.276+11253del		intron variant
NM_001370107.2:c.276+11253del		intron variant
NM_001370108.2:c.276+11253del		intron variant
NM_001370109.2:c.276+11253del		intron variant
NM_001370110.2:c.276+11253del		intron variant
NM_001370111.2:c.276+11253del		intron variant
NM_001370112.2:c.332del	NP_001357041.1:p.Ser111fs	frameshift
NM_001370113.2:c.383del	NP_001357042.1:p.Ser128fs	frameshift
NM_001370114.2:c.383del	NP_001357043.1:p.Ser128fs	frameshift
NM_001370115.2:c.383del	NP_001357044.1:p.Ser128fs	frameshift
NM_001370116.2:c.317del	NP_001357045.1:p.Ser106fs	frameshift
NM_001370117.2:c.383del	NP_001357046.1:p.Ser128fs	frameshift
NM_001370118.2:c.263del	NP_001357047.1:p.Ser88fs	frameshift
NM_001370119.2:c.383del	NP_001357048.1:p.Ser128fs	frameshift
NM_001370120.2:c.210+11253del		intron variant
NM_001370121.2:c.156+11253del		intron variant
NM_001370122.2:c.276+11253del		intron variant
NM_001370123.2:c.225+11253del		intron variant
NM_001370124.3:c.-33-15537del		intron variant
NM_006624.7:c.383del	NP_006615.2:p.Ser128fs	frameshift
NM_212479.4:c.383del	NP_997644.2:p.Ser128fs	frameshift
NR_163254.2:n.470del		non-coding transcript variant
NC_000010.11:g.221301del
NC_000010.10:g.267241del
NG_029960.1:g.91837del

... more HGVS ... less HGVS

Protein change

S128fs, S88fs, S106fs, S111fs

Other names

Canonical SPDI

NC_000010.11:221300:C:

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

RNA degradation by nonsense-mediated decay; Variation Ontology [ VariO:0347]

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: CA645372877 dbSNP: rs1135401771 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)	criteria provided, single submitter	Aug 1, 2017	RCV000496105.2

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 (Aug 01, 2017)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Intellectual disability, autosomal dominant 30 (Autosomal dominant inheritance) Affected status: yes Allele origin: paternal	Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg Accession: SCV000586712.1 First in ClinVar: Aug 05, 2017 Last updated: Aug 05, 2017	Comment: LOF variant in a patient with feeding difficulties, severe ID, febrile seizures, epilepsy, aggressivity, obesity, macrocephaly, hypotonia, ataxic gait. Variant was inherited from the milder … (more) LOF variant in a patient with feeding difficulties, severe ID, febrile seizures, epilepsy, aggressivity, obesity, macrocephaly, hypotonia, ataxic gait. Variant was inherited from the milder affected father. (less) Clinical Features: Intellectual disability (present) Sex: female

Germline Functional Evidence

Functional Help The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence	Method Help A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter.	Result Help A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
RNA degradation by nonsense-mediated decay (VariO:0347)			Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg Accession: SCV000586712.1

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs1135401771 ...

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 Jun 23, 2024

ClinVar Genomic variation as it relates to human health

NM_001370100.5(ZMYND11):c.383del (p.Ser128fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1135401771 ...