rs1131692255
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The NM_003901.4(SGPL1):c.664C>T(p.Arg222Trp) 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 1,461,400 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 (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R222Q) has been classified as Pathogenic.
Frequency
Consequence
NM_003901.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGPL1 | NM_003901.4 | c.664C>T | p.Arg222Trp | missense_variant | 8/15 | ENST00000373202.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGPL1 | ENST00000373202.8 | c.664C>T | p.Arg222Trp | missense_variant | 8/15 | 1 | NM_003901.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251068Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135708
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461400Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726992
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Nephrotic syndrome 14 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at