rs775637217
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015231.3(NUP160):c.2305G>A(p.Glu769Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
NUP160
NM_015231.3 missense
NM_015231.3 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 3.19
Genes affected
NUP160 (HGNC:18017): (nucleoporin 160) A structural constituent of nuclear pore. Involved in mRNA export from nucleus and nephron development. Part of nuclear pore outer ring. Colocalizes with kinetochore. Implicated in nephrotic syndrome type 19. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP160 | NM_015231.3 | c.2305G>A | p.Glu769Lys | missense_variant | 19/36 | ENST00000378460.7 | |
NUP160 | NR_134636.3 | n.2352G>A | non_coding_transcript_exon_variant | 19/36 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP160 | ENST00000378460.7 | c.2305G>A | p.Glu769Lys | missense_variant | 19/36 | 1 | NM_015231.3 | P1 | |
NUP160 | ENST00000694866.1 | c.2407G>A | p.Glu803Lys | missense_variant | 19/36 | ||||
NUP160 | ENST00000530326.5 | c.2302G>A | p.Glu768Lys | missense_variant | 19/34 | 5 | |||
NUP160 | ENST00000528071.5 | c.2305G>A | p.Glu769Lys | missense_variant | 19/28 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251206Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135750
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GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460036Hom.: 0 Cov.: 28 AF XY: 0.00000551 AC XY: 4AN XY: 726494
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ClinVar
Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Nephrotic syndrome, type 19 Pathogenic:1Uncertain:2
Uncertain significance, criteria provided, single submitter | research | Precision Medicine Center, Zhengzhou University | - | PM2:at extremely low frequency in gnomAD - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 31, 2024 | - - |
Uncertain significance, criteria provided, single submitter | curation | SIB Swiss Institute of Bioinformatics | Jan 10, 2019 | This variant is interpreted as a Uncertain significance for Nephrotic syndrome 19, autosomal recessive. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Gain of ubiquitination at E803 (P = 0.0155);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 31
Find out detailed SpliceAI scores and Pangolin per-transcript scores at