NM_016122.3(CEP83):c.662G>A (p.Cys221Tyr) AND Nephronophthisis 18

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 5, 2022
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:: RCV001900392.4

Allele description [Variation Report for NM_016122.3(CEP83):c.662G>A (p.Cys221Tyr)]

NM_016122.3(CEP83):c.662G>A (p.Cys221Tyr)

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.662G>A (p.Cys221Tyr)

HGVS:

NC_000012.12:g.94378930C>T
NG_051825.1:g.86059G>A
NM_001042399.2:c.662G>A
NM_001346457.2:c.662G>A
NM_001346458.2:c.350G>A
NM_001346459.2:c.350G>A
NM_001346460.2:c.662G>A
NM_001346461.2:c.662G>A
NM_001346462.2:c.350G>A
NM_001368037.1:c.662G>A
NM_001368038.1:c.662G>A
NM_001368039.1:c.350G>A
NM_001368040.1:c.350G>A
NM_001368041.1:c.437G>A
NM_001368042.1:c.125G>A
NM_016122.3:c.662G>AMANE SELECT
NP_001035858.1:p.Cys221Tyr
NP_001333386.1:p.Cys221Tyr
NP_001333387.1:p.Cys117Tyr
NP_001333388.1:p.Cys117Tyr
NP_001333389.1:p.Cys221Tyr
NP_001333390.1:p.Cys221Tyr
NP_001333391.1:p.Cys117Tyr
NP_001354966.1:p.Cys221Tyr
NP_001354967.1:p.Cys221Tyr
NP_001354968.1:p.Cys117Tyr
NP_001354969.1:p.Cys117Tyr
NP_001354970.1:p.Cys146Tyr
NP_001354971.1:p.Cys42Tyr
NP_057206.2:p.Cys221Tyr
NC_000012.11:g.94772706C>T
NR_144441.2:n.1012G>A
NR_160431.1:n.928G>A
NR_160432.1:n.1415G>A

Protein change:

C117Y

Links:

dbSNP: rs1289383879

NCBI 1000 Genomes Browser:

rs1289383879

Molecular consequence:

NM_001042399.2:c.662G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001346457.2:c.662G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001346458.2:c.350G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001346459.2:c.350G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001346460.2:c.662G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001346461.2:c.662G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001346462.2:c.350G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368037.1:c.662G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368038.1:c.662G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368039.1:c.350G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368040.1:c.350G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368041.1:c.437G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368042.1:c.125G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_016122.3:c.662G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_144441.2:n.1012G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_160431.1:n.928G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_160432.1:n.1415G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

Recent activity

Clear Turn Off Turn On

CD47 CD47 molecule [Homo sapiens]
CD47 CD47 molecule [Homo sapiens]
Gene ID:961

Gene
Gene Links for GEO Profiles (Select 77967340) (1)
Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002138448	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 5, 2022)	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

SCV002138448

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 5, 2022)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002138448.3

#	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 missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The tyrosine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1373524). This variant has not been reported in the literature in individuals affected with CEP83-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces cysteine with tyrosine at codon 221 of the CEP83 protein (p.Cys221Tyr). The cysteine residue is weakly conserved and there is a large physicochemical difference between cysteine and tyrosine.

#	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

ClinVar

Relating variation to medicine