1-179561355-G-A
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PVS1PM2PP3PP5_Very_Strong
The NM_014625.4(NPHS2):c.385C>T(p.Gln129Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,456,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_014625.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHS2 | NM_014625.4 | c.385C>T | p.Gln129Ter | stop_gained | 3/8 | ENST00000367615.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHS2 | ENST00000367615.9 | c.385C>T | p.Gln129Ter | stop_gained | 3/8 | 1 | NM_014625.4 | P1 | |
NPHS2 | ENST00000367616.4 | c.385C>T | p.Gln129Ter | stop_gained | 3/7 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251256Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135828
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1456074Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 724836
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Nephrotic syndrome, type 2 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Nov 12, 2017 | - - |
Pathogenic, criteria provided, single submitter | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 14, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at