NM_173543.3(DZIP1L):c.1000-4T>C AND Polycystic kidney disease 5

Germline classification:: Uncertain significance (1 submission)
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:: RCV003340685.2

Allele description [Variation Report for NM_173543.3(DZIP1L):c.1000-4T>C]

NM_173543.3(DZIP1L):c.1000-4T>C

Gene:

DZIP1L:DAZ interacting zinc finger protein 1 like [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q22.3

Genomic location:

Preferred name:

NM_173543.3(DZIP1L):c.1000-4T>C

HGVS:

NC_000003.12:g.138087027A>G
NM_001170538.1:c.1000-4T>C
NM_173543.3:c.1000-4T>CMANE SELECT
NC_000003.11:g.137805869A>G

Molecular consequence:

NM_001170538.1:c.1000-4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_173543.3:c.1000-4T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Polycystic kidney disease 5
Identifiers:: MONDO: MONDO:0033281; MedGen: C4539903; OMIM: 617610

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004047326	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV004047326

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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 Neuberg Centre For Genomic Medicine, NCGM, SCV004047326.1

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

Description

The splice region variant c.1000-4T>C in DZIP1L (NM_173543.3) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1000-4T>C variant is observed in 7/30,598 (0.0229%) alleles from individuals of South Asian background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The c.1000-4T>C variant is not predicted to disrupt splicing by any splice site algorithm. The nucleotide c.1000-4T>C in DZIP1L is not conserved according to a GERP++ and PhyloP analysis of 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance

#	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: Apr 6, 2024

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