NM_015021.3(ZNF292):c.6279dup (p.Arg2094fs) AND Intellectual developmental disorder, autosomal dominant 64

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Oct 7, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001810008.2

Allele description

NM_015021.3(ZNF292):c.6279dup (p.Arg2094fs)

Gene:

ZNF292:zinc finger protein 292 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

6q14.3

Genomic location:

Preferred name:

NM_015021.3(ZNF292):c.6279dup (p.Arg2094fs)

HGVS:

NC_000006.12:g.87259908dup
NG_054887.1:g.109358dup
NM_001351444.2:c.5859dup
NM_015021.3:c.6279dupMANE SELECT
NP_001338373.1:p.Arg1954fs
NP_055836.1:p.Arg2094fs
NC_000006.11:g.87969626dup
NM_015021.2:c.6279dup

Protein change:

R1954fs

Links:

dbSNP: rs1775468280

NCBI 1000 Genomes Browser:

rs1775468280

Molecular consequence:

NM_001351444.2:c.5859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015021.3:c.6279dup - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Intellectual developmental disorder, autosomal dominant 64
Synonyms:: MENTAL RETARDATION, AUTOSOMAL DOMINANT 64
Identifiers:: MONDO: MONDO:0030934; MedGen: C5543067; OMIM: 619188

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002059200	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 3, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] PMID:31723249,
SCV003935073	Eurofins-Biomnis	criteria provided, single submitter (Accession Criteria ClinVar Biomnis)	Pathogenic (Oct 7, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002059200

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 3, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

PMID:31723249,

SCV003935073

Eurofins-Biomnis

criteria provided, single submitter

(Accession Criteria ClinVar Biomnis)

Pathogenic
(Oct 7, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	not provided	not provided	2	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 3billion, SCV002059200.1

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

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region (PVS1_S). The variant has been reported to be associated with ZNF292 related disorder (ClinVar ID: VCV000982198, PMID:31723249).It is not observed in the gnomAD v2.1.1 dataset (PM2_M). The variant has been previously reported as de novo in a similarly affected individual (PMID: 31723249, PS2_S). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

From Eurofins-Biomnis, SCV003935073.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jul 1, 2023

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