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NM_014956.5(CEP164):c.2283+2T>C AND Nephronophthisis 15

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 13, 2021
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:
RCV001055384.5

Allele description [Variation Report for NM_014956.5(CEP164):c.2283+2T>C]

NM_014956.5(CEP164):c.2283+2T>C

Gene:
CEP164:centrosomal protein 164 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q23.3
Genomic location:
Preferred name:
NM_014956.5(CEP164):c.2283+2T>C
HGVS:
  • NC_000011.10:g.117391217T>C
  • NG_033032.1:g.74440T>C
  • NM_001271933.2:c.2292+2T>C
  • NM_014956.5:c.2283+2T>CMANE SELECT
  • NC_000011.9:g.117261933T>C
  • NM_014956.4:c.2283+2T>C
Links:
dbSNP: rs1459158279
NCBI 1000 Genomes Browser:
rs1459158279
Molecular consequence:
  • NM_001271933.2:c.2292+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_014956.5:c.2283+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Nephronophthisis 15 (NPHP15)
Identifiers:
MONDO: MONDO:0013917; MedGen: C3541853; Orphanet: 3156; OMIM: 614845

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001219772Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Dec 13, 2021) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling.

Chaki M, Airik R, Ghosh AK, Giles RH, Chen R, Slaats GG, Wang H, Hurd TW, Zhou W, Cluckey A, Gee HY, Ramaswami G, Hong CJ, Hamilton BA, Cervenka I, Ganji RS, Bryja V, Arts HH, van Reeuwijk J, Oud MM, Letteboer SJ, Roepman R, et al.

Cell. 2012 Aug 3;150(3):533-48. doi: 10.1016/j.cell.2012.06.028.

PubMed [citation]
PMID:
22863007
PMCID:
PMC3433835
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV001219772.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 851066). This variant has not been reported in the literature in individuals affected with CEP164-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 17 of the CEP164 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CEP164 are known to be pathogenic (PMID: 22863007, 28125082, 32367404, 34132027, 34499853).

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

Last Updated: Feb 20, 2024