NM_004937.3(CTNS):c.589G>A (p.Gly197Arg) AND multiple conditions

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Apr 8, 2022
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:: RCV000763395.17

Allele description [Variation Report for NM_004937.3(CTNS):c.589G>A (p.Gly197Arg)]

NM_004937.3(CTNS):c.589G>A (p.Gly197Arg)

Genes:

CTNS-AS1:CTNS antisense RNA 1 [Gene - HGNC]
CTNS:cystinosin, lysosomal cystine transporter [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_004937.3(CTNS):c.589G>A (p.Gly197Arg)

HGVS:

NC_000017.11:g.3656703G>A
NG_012489.2:g.25236G>A
NM_001031681.3:c.589G>A
NM_001374492.1:c.589G>A
NM_001374493.1:c.148G>A
NM_001374494.1:c.148G>A
NM_001374495.1:c.148G>A
NM_001374496.1:c.148G>A
NM_004937.3:c.589G>AMANE SELECT
NP_001026851.2:p.Gly197Arg
NP_001361421.1:p.Gly197Arg
NP_001361422.1:p.Gly50Arg
NP_001361423.1:p.Gly50Arg
NP_001361424.1:p.Gly50Arg
NP_001361425.1:p.Gly50Arg
NP_004928.2:p.Gly197Arg
NC_000017.10:g.3559997G>A
NM_004937.2:c.589G>A
O60931:p.Gly197Arg

Protein change:

G197R; GLY197ARG

Links:

UniProtKB: O60931#VAR_010682; OMIM: 606272.0011; dbSNP: rs113994207

NCBI 1000 Genomes Browser:

rs113994207

Molecular consequence:

NM_001031681.3:c.589G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374492.1:c.589G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374493.1:c.148G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374494.1:c.148G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374495.1:c.148G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374496.1:c.148G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004937.3:c.589G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Ocular cystinosis
Synonyms:: Cystinosis, ocular nonnephropathic; Cystinosis, adult, nonnephropathic; Cystinosis, benign, nonnephropathic
Identifiers:: MONDO: MONDO:0009064; MedGen: C2931013; Orphanet: 213; OMIM: 219750

Name:: Juvenile nephropathic cystinosis
Synonyms:: CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE
Identifiers:: MONDO: MONDO:0009066; MedGen: C0268626; Orphanet: 213; Orphanet: 411634; OMIM: 219900

Name:: Nephropathic cystinosis (CTNS)
Synonyms:: CYSTINOSIN, DEFECT OF; LYSOSOMAL CYSTINE TRANSPORT PROTEIN, DEFECT OF; Abderhalden Lignac Kaufmann disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0100151; MedGen: C2931187; Orphanet: 213; Orphanet: 411629; OMIM: 219800

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000894116	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 8, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005418355	Juno Genomics, Hangzhou Juno Genomics, Inc	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	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

SCV000894116

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 8, 2022)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005418355

Juno Genomics, Hangzhou Juno Genomics, Inc

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

PMC

Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]

PMCID:: PMC4544753
PMID:: 25741868
DOI:: 10.1038/gim.2015.30

Details of each submission

From Fulgent Genetics, Fulgent Genetics, SCV000894116.2

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

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

From Juno Genomics, Hangzhou Juno Genomics, Inc, SCV005418355.1

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

Description

PM2_Supporting+PS3_Supporting+PM3_VeryStrong+PP4

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

Last Updated: Jan 13, 2025

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