NM_016122.3(CEP83):c.1451C>A (p.Ser484Ter) AND Nephronophthisis 18

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 23, 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:: RCV001925052.4

Allele description [Variation Report for NM_016122.3(CEP83):c.1451C>A (p.Ser484Ter)]

NM_016122.3(CEP83):c.1451C>A (p.Ser484Ter)

Gene:

CEP83:centrosomal protein 83 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q22

Genomic location:

Preferred name:

NM_016122.3(CEP83):c.1451C>A (p.Ser484Ter)

HGVS:

NC_000012.12:g.94333608G>T
NG_051825.1:g.131381C>A
NM_001042399.2:c.1451C>A
NM_001346457.2:c.1451C>A
NM_001346458.2:c.1139C>A
NM_001346459.2:c.1139C>A
NM_001368037.1:c.1451C>A
NM_001368038.1:c.1451C>A
NM_001368039.1:c.1139C>A
NM_001368040.1:c.1139C>A
NM_001368041.1:c.1226C>A
NM_016122.3:c.1451C>AMANE SELECT
NP_001035858.1:p.Ser484Ter
NP_001333386.1:p.Ser484Ter
NP_001333387.1:p.Ser380Ter
NP_001333388.1:p.Ser380Ter
NP_001354966.1:p.Ser484Ter
NP_001354967.1:p.Ser484Ter
NP_001354968.1:p.Ser380Ter
NP_001354969.1:p.Ser380Ter
NP_001354970.1:p.Ser409Ter
NP_057206.2:p.Ser484Ter
NC_000012.11:g.94727384G>T
NR_160431.1:n.1175C>A
NR_160432.1:n.2196C>A

Protein change:

S380*

Links:

dbSNP: rs777412559

NCBI 1000 Genomes Browser:

rs777412559

Molecular consequence:

NR_160431.1:n.1175C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_160432.1:n.2196C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001042399.2:c.1451C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001346457.2:c.1451C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001346458.2:c.1139C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001346459.2:c.1139C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001368037.1:c.1451C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001368038.1:c.1451C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001368039.1:c.1139C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001368040.1:c.1139C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001368041.1:c.1226C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_016122.3:c.1451C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Nephronophthisis 18 (NPHP18)
Identifiers:: MONDO: MONDO:0014374; MedGen: C3890591; Orphanet: 655; OMIM: 615862

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002169772	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 23, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23530209, 24882706, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002169772

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 23, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

CCDC41 is required for ciliary vesicle docking to the mother centriole.

Joo K, Kim CG, Lee MS, Moon HY, Lee SH, Kim MJ, Kweon HS, Park WY, Kim CH, Gleeson JG, Kim J.

Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):5987-92. doi: 10.1073/pnas.1220927110. Epub 2013 Mar 25.

PubMed [citation]

PMID:: 23530209
PMCID:: PMC3625310

Mutations of CEP83 cause infantile nephronophthisis and intellectual disability.

Failler M, Gee HY, Krug P, Joo K, Halbritter J, Belkacem L, Filhol E, Porath JD, Braun DA, Schueler M, Frigo A, Alibeu O, Masson C, Brochard K, Hurault de Ligny B, Novo R, Pietrement C, Kayserili H, Salomon R, Gubler MC, Otto EA, Antignac C, et al.

Am J Hum Genet. 2014 Jun 5;94(6):905-14. doi: 10.1016/j.ajhg.2014.05.002. Epub 2014 May 29.

PubMed [citation]

PMID:: 24882706
PMCID:: PMC4121475

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002169772.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CEP83-related conditions. This variant is present in population databases (rs777412559, gnomAD 0.01%). This sequence change creates a premature translational stop signal (p.Ser484*) in the CEP83 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CEP83 are known to be pathogenic (PMID: 23530209, 24882706).

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

Last Updated: Sep 29, 2024

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