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NM_006383.4(CIB2):c.300_309del (p.Glu100fs) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Jan 11, 2024
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:
RCV001225372.7

Allele description

NM_006383.4(CIB2):c.300_309del (p.Glu100fs)

Gene:
CIB2:calcium and integrin binding family member 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
15q25.1
Genomic location:
Preferred name:
NM_006383.4(CIB2):c.300_309del (p.Glu100fs)
HGVS:
  • NC_000015.10:g.78109272_78109281del
  • NG_033006.1:g.27255_27264del
  • NM_001271888.2:c.171_180del
  • NM_001271889.2:c.153_162del
  • NM_001301224.2:c.315_324del
  • NM_006383.4:c.300_309delMANE SELECT
  • NP_001258817.1:p.Glu57fs
  • NP_001258818.1:p.Glu51fs
  • NP_001288153.1:p.Glu105fs
  • NP_006374.1:p.Glu100fs
  • NC_000015.9:g.78401614_78401623del
  • NC_000015.9:g.78401614_78401623delGGGAGCCGAC
  • NM_006383.2:c.300_309delGTCGGCTCCC
  • NM_006383.3:c.300_309del
  • NM_006383.3:c.300_309delGTCGGCTCCC
  • NR_125435.2:n.508_517del
  • p.Glu100AspfsX28
Protein change:
E100fs
Links:
dbSNP: rs765741202
NCBI 1000 Genomes Browser:
rs765741202
Molecular consequence:
  • NM_001271888.2:c.171_180del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001271889.2:c.153_162del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001301224.2:c.315_324del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_006383.4:c.300_309del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_125435.2:n.508_517del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001397652Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 11, 2024) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV001772215GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(May 28, 2021) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Novel and recurrent CIB2 variants, associated with nonsyndromic deafness, do not affect calcium buffering and localization in hair cells.

Seco CZ, Giese AP, Shafique S, Schraders M, Oonk AM, Grossheim M, Oostrik J, Strom T, Hegde R, van Wijk E, Frolenkov GI, Azam M, Yntema HG, Free RH, Riazuddin S, Verheij JB, Admiraal RJ, Qamar R, Ahmed ZM, Kremer H.

Eur J Hum Genet. 2016 Apr;24(4):542-9. doi: 10.1038/ejhg.2015.157. Epub 2015 Jul 15.

PubMed [citation]
PMID:
26173970
PMCID:
PMC4929876

Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort.

Bademci G, Foster J 2nd, Mahdieh N, Bonyadi M, Duman D, Cengiz FB, Menendez I, Diaz-Horta O, Shirkavand A, Zeinali S, Subasioglu A, Tokgoz-Yilmaz S, Huesca-Hernandez F, de la Luz Arenas-Sordo M, Dominguez-Aburto J, Hernandez-Zamora E, Montenegro P, Paredes R, Moreta G, Vinueza R, Villegas F, Mendoza-Benitez S, et al.

Genet Med. 2016 Apr;18(4):364-71. doi: 10.1038/gim.2015.89. Epub 2015 Jul 30. Erratum in: Genet Med. 2016 Aug;18(8):859. doi: 10.1038/gim.2016.84.

PubMed [citation]
PMID:
26226137
PMCID:
PMC4733433
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001397652.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Glu100Aspfs*28) in the CIB2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CIB2 are known to be pathogenic (PMID: 26173970, 26226137, 26445815). This variant is present in population databases (rs765741202, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with autosomal recessive deafness (PMID: 29112224). ClinVar contains an entry for this variant (Variation ID: 505395). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001772215.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 29112224, 31589614)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024