rs180177362
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM4PP3PP5
The NM_017890.5(VPS13B):c.5215_5232del(p.Ser1739_Gln1744del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,642 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. L1738L) has been classified as Likely benign.
Frequency
Consequence
NM_017890.5 inframe_deletion
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 |
---|---|---|---|---|---|---|---|
VPS13B | NM_017890.5 | c.5215_5232del | p.Ser1739_Gln1744del | inframe_deletion | 33/62 | ENST00000358544.7 | |
VPS13B | NM_152564.5 | c.5140_5157del | p.Ser1714_Gln1719del | inframe_deletion | 33/62 | ENST00000357162.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000357162.7 | c.5140_5157del | p.Ser1714_Gln1719del | inframe_deletion | 33/62 | 1 | NM_152564.5 | P1 | |
VPS13B | ENST00000358544.7 | c.5215_5232del | p.Ser1739_Gln1744del | inframe_deletion | 33/62 | 1 | NM_017890.5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461642Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 727124
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | SNPedia | - | - - |
Cohen syndrome Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at