NM_000537.4(REN):c.36GCT[3] (p.Leu16del) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 17, 2023
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:: RCV003565383.1

Allele description [Variation Report for NM_000537.4(REN):c.36GCT[3] (p.Leu16del)]

NM_000537.4(REN):c.36GCT[3] (p.Leu16del)

Genes:

LOC107548112:REN promoter and enhancer region [Gene]
REN:renin [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

1q32.1

Genomic location:

Preferred name:

NM_000537.4(REN):c.36GCT[3] (p.Leu16del)

HGVS:

NC_000001.11:g.204166249CAG[3]
NG_012122.1:g.5080GCT[3]
NG_046884.1:g.4184CAG[3]
NM_000537.4:c.36GCT[3]MANE SELECT
NP_000528.1:p.Leu16del
NC_000001.10:g.204135375_204135377del
NC_000001.10:g.204135377CAG[3]
NM_000537.3:c.45_47delGCT
NM_000537.4:c.45_47delMANE SELECT

Note:

ClinGen staff contributed the HGVS expression for this variant.

Protein change:

L16del

Links:

OMIM: 179820.0004; dbSNP: rs1571652012

NCBI 1000 Genomes Browser:

rs1571652012

Molecular consequence:

NM_000537.4:c.36GCT[3] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004320812	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 17, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19664745, 32750457, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004320812

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 17, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Dominant renin gene mutations associated with early-onset hyperuricemia, anemia, and chronic kidney failure.

Zivná M, Hůlková H, Matignon M, Hodanová K, Vylet'al P, Kalbácová M, Baresová V, Sikora J, Blazková H, Zivný J, Ivánek R, Stránecký V, Sovová J, Claes K, Lerut E, Fryns JP, Hart PS, Hart TC, Adams JN, Pawtowski A, Clemessy M, Gasc JM, et al.

Am J Hum Genet. 2009 Aug;85(2):204-13. doi: 10.1016/j.ajhg.2009.07.010. Epub 2009 Aug 6.

PubMed [citation]

PMID:: 19664745
PMCID:: PMC2725269

An international cohort study of autosomal dominant tubulointerstitial kidney disease due to REN mutations identifies distinct clinical subtypes.

Živná M, Kidd K, Zaidan M, Vyleťal P, Barešová V, Hodaňová K, Sovová J, Hartmannová H, Votruba M, Trešlová H, Jedličková I, Sikora J, Hůlková H, Robins V, Hnízda A, Živný J, Papagregoriou G, Mesnard L, Beck BB, Wenzel A, Tory K, Häeffner K, et al.

Kidney Int. 2020 Dec;98(6):1589-1604. doi: 10.1016/j.kint.2020.06.041. Epub 2020 Aug 1.

PubMed [citation]

PMID:: 32750457
PMCID:: PMC7719087

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004320812.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this variant affects REN function (PMID: 19664745, 32750457). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 13125). This variant has been observed in individuals with autosomal dominant tubulointerstitial kidney disease (PMID: 19664745, 32750457). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This variant, c.45_47del, results in the deletion of 1 amino acid(s) of the REN protein (p.Leu16del), but otherwise preserves the integrity of the reading frame.

#	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: Feb 20, 2024

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