chr19-47476636-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007059.4(KPTN):c.1078C>T(p.Arg360Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000775 in 1,612,400 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R360Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_007059.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KPTN | NM_007059.4 | c.1078C>T | p.Arg360Trp | missense_variant | 11/12 | ENST00000338134.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KPTN | ENST00000338134.8 | c.1078C>T | p.Arg360Trp | missense_variant | 11/12 | 1 | NM_007059.4 | P1 | |
ENST00000669287.1 | n.243G>A | non_coding_transcript_exon_variant | 2/2 | ||||||
KPTN | ENST00000594208.5 | c.*712C>T | 3_prime_UTR_variant, NMD_transcript_variant | 12/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000529 AC: 8AN: 151278Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.0000407 AC: 10AN: 245412Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133992
GnomAD4 exome AF: 0.0000801 AC: 117AN: 1461122Hom.: 0 Cov.: 31 AF XY: 0.0000881 AC XY: 64AN XY: 726858
GnomAD4 genome AF: 0.0000529 AC: 8AN: 151278Hom.: 0 Cov.: 26 AF XY: 0.0000677 AC XY: 5AN XY: 73802
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.1078C>T (p.R360W) alteration is located in exon 11 (coding exon 11) of the KPTN gene. This alteration results from a C to T substitution at nucleotide position 1078, causing the arginine (R) at amino acid position 360 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at