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NM_001023570.4(IQCB1):c.758del (p.Cys253fs) AND Nephronophthisis

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 2, 2018
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001328085.1

Allele description [Variation Report for NM_001023570.4(IQCB1):c.758del (p.Cys253fs)]

NM_001023570.4(IQCB1):c.758del (p.Cys253fs)

Gene:
IQCB1:IQ motif containing B1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3q13.33
Genomic location:
Preferred name:
NM_001023570.4(IQCB1):c.758del (p.Cys253fs)
HGVS:
  • NC_000003.12:g.121799204del
  • NG_015887.1:g.40876del
  • NM_001023570.4:c.758delMANE SELECT
  • NM_001023571.4:c.587+8140del
  • NM_001319107.2:c.758del
  • NP_001018864.2:p.Cys253fs
  • NP_001306036.1:p.Cys253fs
  • NC_000003.11:g.121518051del
  • NM_001023570.3:c.758del
  • NR_134968.2:n.953del
Protein change:
C253fs
Links:
dbSNP: rs770441610
NCBI 1000 Genomes Browser:
rs770441610
Molecular consequence:
  • NM_001023570.4:c.758del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001319107.2:c.758del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001023571.4:c.587+8140del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_134968.2:n.953del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Nephronophthisis
Synonyms:
juvenile nephronophthisis
Identifiers:
MONDO: MONDO:0019005; MedGen: C0687120; OMIM: PS256100; Human Phenotype Ontology: HP:0000090

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001449344Sydney Genome Diagnostics, Children's Hospital Westmead
no assertion criteria provided
Likely pathogenic
(Mar 2, 2018) 		unknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Sydney Genome Diagnostics, Children's Hospital Westmead, SCV001449344.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

This patient is also heterozygous for a 4 bp duplication, c.897_900dup, in the IQCB1 gene. This frameshifting variant is predicted to create a premature stop codon p.(Ile301Leufs*42) and may result in a null allele due to nonsense-mediated mRNA decay. This variant has been listed in the ExAC database (http://exac.broadinstitute.org) with a low allele frequency of 0.01% (8 out of 66,560 alleles). The c.897_900dup variant has been reported in a compound heterozygous state with another truncating variant in a patient with Senior-Loken syndrome (Halbritter et al. 2012 J Med Genet 49:756-767). This variant is considered to be likely pathogenic according to the ACMG guidelines.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Dec 30, 2023