rs1295123083
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_007059.4(KPTN):c.665dupA(p.Ser223fs) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000258 in 1,549,446 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
KPTN
NM_007059.4 frameshift
NM_007059.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.27
Genes affected
KPTN (HGNC:6404): (kaptin, actin binding protein) This gene encodes a filamentous-actin-associated protein, which is involved in actin dynamics and plays an important role in neuromorphogenesis. This protein is part of the KICSTOR protein complex that localizes to lysosomes. Mutations in this gene result in an autosomal recessive form of intellectual disability. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 19-47480341-C-CT is Pathogenic according to our data. Variant chr19-47480341-C-CT is described in ClinVar as [Pathogenic]. Clinvar id is 504486.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KPTN | NM_007059.4 | c.665dupA | p.Ser223fs | frameshift_variant | 7/12 | ENST00000338134.8 | NP_008990.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000662 AC: 1AN: 150952Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.00000215 AC: 3AN: 1398494Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 689756
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GnomAD4 genome AF: 0.00000662 AC: 1AN: 150952Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 73702
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Macrocephaly-developmental delay syndrome Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 06, 2019 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 06, 2022 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at