rs1555487621

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate

The NM_003361.4(UMOD):​c.358T>G​(p.Cys120Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C120F) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 33)

Consequence

UMOD
NM_003361.4 missense

Scores

12
4
3

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 5.54
Variant links:
Genes affected
UMOD (HGNC:12559): (uromodulin) The protein encoded by this gene is the most abundant protein in mammalian urine under physiological conditions. Its excretion in urine follows proteolytic cleavage of the ectodomain of its glycosyl phosphatidylinosital-anchored counterpart that is situated on the luminal cell surface of the loop of Henle. This protein may act as a constitutive inhibitor of calcium crystallization in renal fluids. Excretion of this protein in urine may provide defense against urinary tract infections caused by uropathogenic bacteria. Defects in this gene are associated with the renal disorders medullary cystic kidney disease-2 (MCKD2), glomerulocystic kidney disease with hyperuricemia and isosthenuria (GCKDHI), and familial juvenile hyperuricemic nephropathy (FJHN). Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2013]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PM1
In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 4 uncertain in NM_003361.4
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr16-20348942-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3066135.Status of the report is criteria_provided_single_submitter, 1 stars.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.991
PP5
Variant 16-20348943-A-C is Pathogenic according to our data. Variant chr16-20348943-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 488632.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UMODNM_003361.4 linkuse as main transcriptc.358T>G p.Cys120Gly missense_variant 3/11 ENST00000396138.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UMODENST00000396138.9 linkuse as main transcriptc.358T>G p.Cys120Gly missense_variant 3/115 NM_003361.4 P2P07911-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
39
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Familial juvenile hyperuricemic nephropathy type 1 Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingInstitute of Human Genetics Munich, Klinikum Rechts Der Isar, TU MünchenNov 08, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.81
BayesDel_addAF
Pathogenic
0.54
D
BayesDel_noAF
Pathogenic
0.54
CADD
Uncertain
26
DANN
Benign
0.96
DEOGEN2
Pathogenic
0.80
.;.;.;.;D;.
Eigen
Pathogenic
0.73
Eigen_PC
Uncertain
0.61
FATHMM_MKL
Uncertain
0.81
D
LIST_S2
Benign
0.78
T;T;T;.;T;T
M_CAP
Pathogenic
0.93
D
MetaRNN
Pathogenic
0.99
D;D;D;D;D;D
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Pathogenic
4.3
.;.;H;H;.;.
MutationTaster
Benign
0.76
D;D;D;D;D;D
PrimateAI
Uncertain
0.54
T
PROVEAN
Pathogenic
-5.6
D;.;D;.;.;.
REVEL
Pathogenic
0.89
Sift
Pathogenic
0.0
D;.;D;.;.;.
Sift4G
Uncertain
0.0060
D;D;D;D;.;.
Polyphen
1.0
.;.;D;D;.;.
Vest4
0.96
MutPred
0.98
.;.;Loss of stability (P = 0.0079);Loss of stability (P = 0.0079);.;Loss of stability (P = 0.0079);
MVP
0.82
MPC
2.1
ClinPred
0.99
D
GERP RS
5.5
Varity_R
0.98
gMVP
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1555487621; hg19: chr16-20360265; API