NM_016122.3(CEP83):c.614A>G (p.Lys205Arg) AND Nephronophthisis 18

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 23, 2020
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:: RCV001966725.4

Allele description [Variation Report for NM_016122.3(CEP83):c.614A>G (p.Lys205Arg)]

NM_016122.3(CEP83):c.614A>G (p.Lys205Arg)

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.614A>G (p.Lys205Arg)

HGVS:

NC_000012.12:g.94378978T>C
NG_051825.1:g.86011A>G
NM_001042399.2:c.614A>G
NM_001346457.2:c.614A>G
NM_001346458.2:c.302A>G
NM_001346459.2:c.302A>G
NM_001346460.2:c.614A>G
NM_001346461.2:c.614A>G
NM_001346462.2:c.302A>G
NM_001368037.1:c.614A>G
NM_001368038.1:c.614A>G
NM_001368039.1:c.302A>G
NM_001368040.1:c.302A>G
NM_001368041.1:c.389A>G
NM_001368042.1:c.77A>G
NM_016122.3:c.614A>GMANE SELECT
NP_001035858.1:p.Lys205Arg
NP_001333386.1:p.Lys205Arg
NP_001333387.1:p.Lys101Arg
NP_001333388.1:p.Lys101Arg
NP_001333389.1:p.Lys205Arg
NP_001333390.1:p.Lys205Arg
NP_001333391.1:p.Lys101Arg
NP_001354966.1:p.Lys205Arg
NP_001354967.1:p.Lys205Arg
NP_001354968.1:p.Lys101Arg
NP_001354969.1:p.Lys101Arg
NP_001354970.1:p.Lys130Arg
NP_001354971.1:p.Lys26Arg
NP_057206.2:p.Lys205Arg
NC_000012.11:g.94772754T>C
NR_144441.2:n.964A>G
NR_160431.1:n.880A>G
NR_160432.1:n.1367A>G

Protein change:

K101R

Links:

dbSNP: rs1566032936

NCBI 1000 Genomes Browser:

rs1566032936

Molecular consequence:

NM_001042399.2:c.614A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346457.2:c.614A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346458.2:c.302A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346459.2:c.302A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346460.2:c.614A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346461.2:c.614A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346462.2:c.302A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368037.1:c.614A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368038.1:c.614A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368039.1:c.302A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368040.1:c.302A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368041.1:c.389A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368042.1:c.77A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_016122.3:c.614A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_144441.2:n.964A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_160431.1:n.880A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_160432.1:n.1367A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV002257088	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 23, 2020)	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

SCV002257088

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 23, 2020)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002257088.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The arginine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with CEP83-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces lysine with arginine at codon 205 of the CEP83 protein (p.Lys205Arg). The lysine residue is weakly conserved and there is a small physicochemical difference between lysine and arginine.

#	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: Mar 5, 2024

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