VCV000094083.30 - ClinVar

NM_002764.4(PRPS1):c.477C>T (p.Ile159=)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(17)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_002764.4(PRPS1):c.477C>T (p.Ile159=)

Variation ID: 94083 Accession: VCV000094083.30

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: Xq22.3 X: 107642437 (GRCh38) [ NCBI UCSC ] X: 106885667 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 2, 2016	Sep 29, 2024	Feb 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_002764.4:c.477C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_002755.1:p.Ile159=	synonymous
NM_001204402.2:c.-82-2740C>T		intron variant
NC_000023.11:g.107642437C>T
NC_000023.10:g.106885667C>T
NG_008407.1:g.19014C>T
LRG_264:g.19014C>T
LRG_264t1:c.477C>T	LRG_264p1:p.Ile159=

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000023.11:107642436:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00503 (T)

Allele frequency Help The frequency of the allele represented by this VCV record.

1000 Genomes Project 0.00503

1000 Genomes Project 30x 0.00541

Trans-Omics for Precision Medicine (TOPMed) 0.00555

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00596

The Genome Aggregation Database (gnomAD) 0.00596

The Genome Aggregation Database (gnomAD), exomes 0.00746

Exome Aggregation Consortium (ExAC) 0.00811

Links

ClinGen: CA147596 dbSNP: rs61752962 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
PRPS1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	307	476

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Benign (4)	criteria provided, multiple submitters, no conflicts	Feb 19, 2014	RCV000080032.17
Charcot-Marie-Tooth Neuropathy X	Benign (1)	criteria provided, single submitter	Feb 1, 2024	RCV000204144.14
Arts syndrome	Benign (2)	criteria provided, multiple submitters, no conflicts	Oct 25, 2021	RCV000308646.7
Hearing loss, X-linked 1	Benign (2)	criteria provided, multiple submitters, no conflicts	Oct 25, 2021	RCV000362584.7
Phosphoribosylpyrophosphate synthetase superactivity	Benign (2)	criteria provided, multiple submitters, no conflicts	Oct 25, 2021	RCV000402522.7
not provided	Benign (4)	criteria provided, multiple submitters, no conflicts	Oct 18, 2023	RCV001664331.8
Charcot-Marie-Tooth disease X-linked recessive 5	Benign (1)	criteria provided, single submitter	Oct 25, 2021	RCV001789127.2
Arts syndrome Charcot-Marie-Tooth disease X-linked recessive 5 Hearing loss, X-linked 1 Phosphoribosylpyrophosphate synthetase superactivity	Likely benign (1)	criteria provided, single submitter	Jul 21, 2021	RCV002498407.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NOT SPECIFIED Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV000309180.1 First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016
Benign (Feb 19, 2014)	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000111926.8 First in ClinVar: Jan 23, 2014 Last updated: Oct 02, 2016	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PRPS1 http://www.ncbi.nlm.nih.gov/vari… http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?chr=X&from=106885667&to=106885667 Number of individuals with the variant: 1 Sex: mixed
Benign (May 07, 2012)	criteria provided, single submitter (LMM Criteria) Method: clinical testing	not specified Affected status: not provided Allele origin: germline	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine Accession: SCV000199989.5 First in ClinVar: Jan 30, 2015 Last updated: Oct 02, 2016	Comment: "Ile159Ile in Exon 04 of PRPS1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, … (more) "Ile159Ile in Exon 04 of PRPS1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 0.8% (42/5545) of Eu ropean American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs61752962)." (less) Number of individuals with the variant: 17
Benign (Mar 03, 2015)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001874703.1 First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021
Likely benign (Jul 21, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Phosphoribosylpyrophosphate synthetase superactivity Arts syndrome Hearing loss, X-linked 1 Charcot-Marie-Tooth disease X-linked recessive 5 Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV002805045.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022
Benign (Feb 01, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Charcot-Marie-Tooth Neuropathy X Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000262494.11 First in ClinVar: Jan 31, 2016 Last updated: Feb 20, 2024
Benign (Jan 13, 2018)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Hearing loss, X-linked 1 Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000481430.3 First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020	Comment: This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more) This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
Benign (Jan 13, 2018)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Phosphoribosylpyrophosphate synthetase superactivity Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000481431.3 First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020	Comment: This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more) This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
Benign (Jan 13, 2018)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Arts syndrome Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000481432.3 First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020	Comment: This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more) This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
Benign (Oct 25, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Arts syndrome Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV002031950.1 First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021
Benign (Oct 25, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Charcot-Marie-Tooth disease X-linked recessive 5 Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV002031951.1 First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021
Benign (Oct 25, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Hearing loss, X-linked 1 Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV002031953.1 First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021
Benign (Oct 25, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Phosphoribosylpyrophosphate synthetase superactivity Affected status: no Allele origin: germline	Genome-Nilou Lab Accession: SCV002031954.1 First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021
Benign (Oct 18, 2023)	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories Accession: SCV003799602.3 First in ClinVar: Feb 13, 2023 Last updated: Feb 20, 2024
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (X-linked inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005276404.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	Clinical Genetics, Academic Medical Center Additional submitter: Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001918956.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021
Likely benign (-)	no assertion criteria provided Method: clinical testing	not provided Affected status: yes Allele origin: germline	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001963181.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021
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Comment:

"Ile159Ile in Exon 04 of PRPS1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 0.8% (42/5545) of Eu ropean American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs61752962)."

Comment:

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

Comment:

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PRPS1	-	-	-	-

Text-mined citations for rs61752962 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_002764.4(PRPS1):c.477C>T (p.Ile159=)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs61752962 ...