VCV000633661.4 - ClinVar

NM_144773.4(PROKR2):c.332T>G (p.Met111Arg)

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.

(4)

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.

Conflicting classifications of pathogenicity
Likely pathogenic(2); Uncertain significance(2)

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_144773.4(PROKR2):c.332T>G (p.Met111Arg)

Variation ID: 633661 Accession: VCV000633661.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 20p12.3 20: 5314038 (GRCh38) [ NCBI UCSC ] 20: 5294684 (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	Jun 9, 2019	Mar 28, 2022	Mar 8, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NM_144773.4:c.332T>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_658986.1:p.Met111Arg	missense
NC_000020.11:g.5314038A>C
NC_000020.10:g.5294684A>C
NG_008132.2:g.5332T>G

Protein change

M111R

Other names

Canonical SPDI

NC_000020.11:5314037:A:C

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.

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

The Genome Aggregation Database (gnomAD), exomes 0.00000

Trans-Omics for Precision Medicine (TOPMed) 0.00001

Links

dbSNP: rs914930539 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.
PROKR2		-	-	GRCh38 GRCh37	155	192

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 provided	Uncertain significance (1)	no assertion criteria provided	Sep 16, 2018	RCV000782204.1
Hypogonadotropic hypogonadism 3 with or without anosmia	Likely pathogenic (2)	no assertion criteria provided	Feb 14, 2019	RCV001542623.3
Amenorrhea	Uncertain significance (1)	no assertion criteria provided	Mar 8, 2021	RCV001849439.1

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.
Uncertain significance (Sep 16, 2018)	no assertion criteria provided (ACMG Guidelines, 2015) Method: research	not provided Affected status: no Allele origin: germline	Gharavi Laboratory, Columbia University Accession: SCV000920684.1 First in ClinVar: Jun 09, 2019 Last updated: Jun 09, 2019
Likely pathogenic (-)	no assertion criteria provided (ACGS Guidelines, 2016) Method: clinical testing	Hypogonadotropic hypogonadism 3 with or without anosmia Affected status: yes Allele origin: germline	Genomics England Pilot Project, Genomics England Accession: SCV001760468.1 First in ClinVar: Jul 27, 2021 Last updated: Jul 27, 2021
Uncertain significance (Mar 08, 2021)	no assertion criteria provided Method: literature only	Amenorrhea Affected status: yes Allele origin: unknown	Yale Center for Mendelian Genomics, Yale University Study: Yale Center for Mendelian Genomics Accession: SCV002106804.1 First in ClinVar: Mar 28, 2022 Last updated: Mar 28, 2022	Publications: PubMed (1) PubMed: 32870266
Likely pathogenic (Feb 14, 2019)	no assertion criteria provided Method: literature only	Hypogonadotropic hypogonadism 3 with or without anosmia Affected status: yes Allele origin: germline	Yale Center for Mendelian Genomics, Yale University Study: Yale Center for Mendelian Genomics Accession: SCV002106590.1 First in ClinVar: Mar 28, 2022 Last updated: Mar 28, 2022	Publications: PubMed (1) PubMed: 30773290

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Increased Burden of Rare Sequence Variants in GnRH-Associated Genes in Women With Hypothalamic Amenorrhea.	Delaney A	The Journal of clinical endocrinology and metabolism	2021	PMID: 32870266
Monogenic causes of chronic kidney disease in adults.	Connaughton DM	Kidney international	2019	PMID: 30773290

Text-mined citations for rs914930539 ...

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 Jan 07, 2023

ClinVar Genomic variation as it relates to human health

NM_144773.4(PROKR2):c.332T>G (p.Met111Arg)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs914930539 ...