NM_003361.4(UMOD):c.774G>C (p.Trp258Cys) AND Familial juvenile hyperuricemic nephropathy type 1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 19, 2018
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:: RCV002251376.9

Allele description [Variation Report for NM_003361.4(UMOD):c.774G>C (p.Trp258Cys)]

NM_003361.4(UMOD):c.774G>C (p.Trp258Cys)

Gene:

UMOD:uromodulin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p12.3

Genomic location:

Preferred name:

NM_003361.4(UMOD):c.774G>C (p.Trp258Cys)

HGVS:

NC_000016.10:g.20348527C>G
NG_008151.1:g.9189G>C
NM_001008389.3:c.774G>C
NM_001278614.2:c.873G>C
NM_001378232.1:c.774G>C
NM_001378233.1:c.774G>C
NM_001378234.1:c.774G>C
NM_001378235.1:c.774G>C
NM_001378237.1:c.774G>C
NM_003361.4:c.774G>CMANE SELECT
NP_001008390.1:p.Trp258Cys
NP_001265543.1:p.Trp291Cys
NP_001365161.1:p.Trp258Cys
NP_001365162.1:p.Trp258Cys
NP_001365163.1:p.Trp258Cys
NP_001365164.1:p.Trp258Cys
NP_001365166.1:p.Trp258Cys
NP_003352.2:p.Trp258Cys
NP_003352.2:p.Trp258Cys
NC_000016.9:g.20359849C>G
NM_003361.3:c.774G>C
NR_165456.1:n.999G>C

Protein change:

W258C

Links:

dbSNP: rs1567309582

NCBI 1000 Genomes Browser:

rs1567309582

Molecular consequence:

NM_001008389.3:c.774G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001278614.2:c.873G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001378232.1:c.774G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001378233.1:c.774G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001378234.1:c.774G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001378235.1:c.774G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001378237.1:c.774G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003361.4:c.774G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_165456.1:n.999G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Familial juvenile hyperuricemic nephropathy type 1 (ADTKD1)
Synonyms:: Medullary cystic kidney disease 2, autosomal dominant; TUBULOINTERSTITIAL KIDNEY DISEASE, AUTOSOMAL DOMINANT, 1; Glomerulocystic kidney disease with hyperuricemia and isosthenuria; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008073; MedGen: C4551496; Orphanet: 209886; Orphanet: 34149; OMIM: 162000

Recent activity

Clear Turn Off Turn On

KIF-binding protein isoform X1 [Homo sapiens]
KIF-binding protein isoform X1 [Homo sapiens]
gi|1034567662|ref|XP_016871556.1|

Protein

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
SCV001434942	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 19, 2018)	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

SCV001434942

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 19, 2018)

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

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

Details of each submission

From Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine, SCV001434942.1

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

Description

The c.774G>C (p.Trp258Cys) variant in the UMOD gene is identified in a patient with clinical diagnosis of autosomal dominant tubulointerstitial kidney disease referred for genetic testing in our laboratory. This variant segregates with disease in the family. This variant has never been reported in general population databases and is located in a region where most of the variants associated with kidney disease in the UMOD gene are reported (PMID 28781372). Multiple lines of algorithms predict deleterious effect of the p.Trp258Cys change. Therefore, this c.774G>C (p.Trp258Cys) variant in the UMOD gene is classified as likely pathogenic.

#	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: Nov 10, 2024

ClinVar

Relating variation to medicine