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NM_003361.4(UMOD):c.317G>T (p.Cys106Phe) AND UMOD-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 22, 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:
RCV004528290.1

Allele description [Variation Report for NM_003361.4(UMOD):c.317G>T (p.Cys106Phe)]

NM_003361.4(UMOD):c.317G>T (p.Cys106Phe)

Gene:
UMOD:uromodulin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p12.3
Genomic location:
Preferred name:
NM_003361.4(UMOD):c.317G>T (p.Cys106Phe)
HGVS:
  • NC_000016.10:g.20348984C>A
  • NG_008151.1:g.8732G>T
  • NM_001008389.3:c.317G>T
  • NM_001278614.2:c.416G>T
  • NM_001378232.1:c.317G>T
  • NM_001378233.1:c.317G>T
  • NM_001378234.1:c.317G>T
  • NM_001378235.1:c.317G>T
  • NM_001378237.1:c.317G>T
  • NM_003361.4:c.317G>TMANE SELECT
  • NP_001008390.1:p.Cys106Phe
  • NP_001265543.1:p.Cys139Phe
  • NP_001365161.1:p.Cys106Phe
  • NP_001365162.1:p.Cys106Phe
  • NP_001365163.1:p.Cys106Phe
  • NP_001365164.1:p.Cys106Phe
  • NP_001365166.1:p.Cys106Phe
  • NP_003352.2:p.Cys106Phe
  • NP_003352.2:p.Cys106Phe
  • NC_000016.9:g.20360306C>A
  • NM_003361.2:c.317G>T
  • NM_003361.3:c.317G>T
  • NR_165456.1:n.542G>T
Protein change:
C106F
Links:
dbSNP: rs398123697
NCBI 1000 Genomes Browser:
rs398123697
Molecular consequence:
  • NM_001008389.3:c.317G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001278614.2:c.416G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378232.1:c.317G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378233.1:c.317G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378234.1:c.317G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378235.1:c.317G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378237.1:c.317G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003361.4:c.317G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_165456.1:n.542G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
UMOD-related disorder
Synonyms:
UMOD-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004105465PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(May 22, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 PreventionGenetics, part of Exact Sciences, SCV004105465.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The UMOD c.317G>T variant is predicted to result in the amino acid substitution p.Cys106Phe. This variant has been reported in multiple individuals with tubulointerstitial kidney disease (Devuyst et al. 2017. PubMed ID: 28781372; Kim et al. 2017. PubMed ID: 29212948; Table S7, Groopman et al. 2018. PubMed ID: 30586318; Chun et al. 2020. PubMed ID: 32274456; Olinger et al. 2020. PubMed ID: 32450155; Kidd et al. 2020. PubMed ID: 32954071). Functional studies using a mouse model showed that this variant results in autoantibodies against aggregated misfolded protein with immune complex formation and kidney fibrosis (Plotkin et al. 2020. PubMed ID: 32926855). This variant is reported in 0.0026% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/16-20360306-C-A). This variant is interpreted as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024