17-41758746-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_002230.4(JUP):c.1622A>C(p.His541Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000413 in 1,454,212 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002230.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JUP | NM_002230.4 | c.1622A>C | p.His541Pro | missense_variant | Exon 9 of 14 | ENST00000393931.8 | NP_002221.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JUP | ENST00000393931.8 | c.1622A>C | p.His541Pro | missense_variant | Exon 9 of 14 | 1 | NM_002230.4 | ENSP00000377508.3 | ||
JUP | ENST00000310706.9 | c.1622A>C | p.His541Pro | missense_variant | Exon 9 of 15 | 1 | ENSP00000311113.5 | |||
JUP | ENST00000393930.5 | c.1622A>C | p.His541Pro | missense_variant | Exon 9 of 15 | 5 | ENSP00000377507.1 | |||
JUP | ENST00000585793.1 | n.220A>C | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152062Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00000427 AC: 1AN: 234452Hom.: 0 AF XY: 0.00000786 AC XY: 1AN XY: 127238
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1454212Hom.: 0 Cov.: 32 AF XY: 0.00000415 AC XY: 3AN XY: 722870
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74292
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
The p.H541P variant (also known as c.1622A>C), located in coding exon 8 of the JUP gene, results from an A to C substitution at nucleotide position 1622. The histidine at codon 541 is replaced by proline, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at