VCV000585155.4 - ClinVar

NM_015021.3(ZNF292):c.1408A>G (p.Ile470Val)

Germline

Classification

no assertion criteria provided. Learn more about how ClinVar calculates review status.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Uncertain significance(1)

2 out of 3 submissions contributed to this 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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_015021.3(ZNF292):c.1408A>G (p.Ile470Val)

Variation ID: 585155 Accession: VCV000585155.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 6q14.3 6: 87964755 (GRCh37) [ NCBI UCSC ] 6: 87255037 (GRCh38) [ 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	Oct 14, 2018	Apr 13, 2025	Dec 14, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_015021.3:c.1408A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_055836.1:p.Ile470Val	missense
NM_001351444.2:c.988A>G	NP_001338373.1:p.Ile330Val	missense
NC_000006.12:g.87255037A>G
NC_000006.11:g.87964755A>G
NG_054887.1:g.104487A>G

... more HGVS ... less HGVS

Protein change

I470V, I330V

Other names

p.I470V

Canonical SPDI

NC_000006.12:87255036:A:G

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.

Trans-Omics for Precision Medicine (TOPMed) 0.00000

The Genome Aggregation Database (gnomAD) 0.00001

The Genome Aggregation Database (gnomAD), exomes 0.00000

Links

ClinGen: CA364908989 dbSNP: rs1166797338 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.
ZNF292		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	829	877

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.
not provided	not provided (1)	no classification provided	-	RCV000709976.2
Neurodevelopmental disorder	Uncertain significance (1)	no assertion criteria provided	-	RCV001261756.1
Intellectual developmental disorder, autosomal dominant 64	Likely pathogenic (1)	no assertion criteria provided	Dec 14, 2023	RCV003992374.2

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.	Expand all rows Collapse all rows 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.
Uncertain significance (-) C Contributing to aggregate classification	no assertion criteria provided	Neurodevelopmental disorder	University of Washington Center for Mendelian Genomics, University of Washington Accession: SCV001439072.1 First in ClinVar: Oct 25, 2020 Last updated: Oct 25, 2020	Publications: PubMed (1) PubMed: 31723249 Observation: 1 Collection method: research Allele origin: de novo Affected status: yes more Observation 1 Collection method: research Allele origin: de novo Affected status: yes Number of individuals with the variant: 2

Likely pathogenic (Dec 14, 2023) C Contributing to aggregate classification	no assertion criteria provided	Intellectual developmental disorder, autosomal dominant 64	Undiagnosed Diseases Network, NIH Study: Undiagnosed Diseases Network (NIH), UDN Accession: SCV004812037.2 First in ClinVar: Apr 15, 2024 Last updated: Apr 13, 2025	Observation: 1 Collection method: clinical testing Allele origin: de novo Affected status: yes more Observation 1 Collection method: clinical testing Allele origin: de novo Affected status: yes Number of individuals with the variant: 2 Clinical Features: Small for gestational age (present) , Premature birth (present) , Abnormal delivery (present) , Birth length less than 3rd percentile (present) , Premature birth following premature rupture of fetal membranes (present) , Twin-to-twin transfusion (present) , Progressive microcephaly (present) , Agitation (present) , Seizure (present) , Global developmental delay (present) , Cerebellar hypoplasia (present) , Abnormality of the lung (present) , Developmental regression (present) , Aphasia (present) , Inability to walk (present) , Aspiration (present) , Bronchial cartilage hypoplasia (present) , Periventricular leukomalacia (present) , EEG with generalized epileptiform discharges (present) , Feeding difficulties (present) , Hypoplasia of the pons (present) , Chronic constipation (present) , Infantile spasms (present) , Refractory drug response (present) , Grade I preterm intraventricular hemorrhage (present) , Raynaud phenomenon (present) , Twin-to-twin transfusion (present) , Cerebral visual impairment (present) , Insomnia (present) Zygosity: Single Heterozygote Age: 0-9 years Sex: female Tissue: Blood

not provided (-) N Not contributing to aggregate classification	no classification provided	not provided	GenomeConnect, ClinGen Accession: SCV000840341.2 First in ClinVar: Oct 14, 2018 Last updated: Apr 13, 2025	Comment: show GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. (less) Observation: 1 Collection method: phenotyping only Allele origin: de novo Affected status: unknown more Observation 1 Collection method: phenotyping only Allele origin: de novo Affected status: unknown Clinical Features: Abnormality of the umbilical cord (present) , Premature birth (present) , Abnormality of the placenta (present) , Prenatal maternal abnormality (present) , Abnormal delivery (present) , Abnormality of the amniotic fluid (present) , Oral-pharyngeal dysphagia (present) , Abnormality of the skull (present) , Abnormality of the hair (present) , Abnormality of vision (present) , Abnormality of eye movement (present) , Seizures (present) , Encephalopathy (present) , EEG abnormality (present) , Abnormality of coordination (present) , Cognitive impairment (present) , Cerebral palsy (present) , Morphological abnormality of the central nervous system (present) , Generalized hypotonia (present) , Hypertonia (present) , Abnormality of the musculature of the pelvis (present) , Abnormality of the musculature of the limbs (present) , Abnormality of muscle physiology (present) , Decreased pulmonary function (present) , Abnormality of the lung (present) , Gastrointestinal dysmotility (present) , Abnormality of the stomach (present) , Feeding difficulties (present) Indication for testing: Diagnostic Test name: Exome Sequencing Age: 0-9 years Sex: female Testing laboratory: GeneDx Date variant was reported to submitter: 2017-07-18 Testing laboratory interpretation: Uncertain significance

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
De novo and inherited variants in ZNF292 underlie a neurodevelopmental disorder with features of autism spectrum disorder.	Mirzaa GM	Genetics in medicine : official journal of the American College of Medical Genetics	2020	PMID: 31723249

Text-mined citations for rs1166797338 ...

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 Apr 13, 2025