rs1553312393
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_014625.4(NPHS2):c.934C>G(p.Leu312Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,784 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L312L) has been classified as Likely benign.
Frequency
Consequence
NM_014625.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHS2 | NM_014625.4 | c.934C>G | p.Leu312Val | missense_variant | 8/8 | ENST00000367615.9 | |
AXDND1 | NM_144696.6 | c.3032-3121G>C | intron_variant | ENST00000367618.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHS2 | ENST00000367615.9 | c.934C>G | p.Leu312Val | missense_variant | 8/8 | 1 | NM_014625.4 | P1 | |
AXDND1 | ENST00000367618.8 | c.3032-3121G>C | intron_variant | 1 | NM_144696.6 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461784Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727192
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Nephrotic syndrome, type 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | May 10, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at