rs80358268
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Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_006432.5(NPC2):c.190+5G>A variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.0000196 in 1,583,322 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
NPC2
NM_006432.5 splice_donor_5th_base, intron
NM_006432.5 splice_donor_5th_base, intron
Scores
1
1
Splicing: ADA: 1.000
2
Clinical Significance
Conservation
PhyloP100: 6.90
Genes affected
NPC2 (HGNC:14537): (NPC intracellular cholesterol transporter 2) This gene encodes a protein containing a lipid recognition domain. The encoded protein may function in regulating the transport of cholesterol through the late endosomal/lysosomal system. Mutations in this gene have been associated with Niemann-Pick disease, type C2 and frontal lobe atrophy. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 14 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
PP5
Variant 14-74486324-C-T is Pathogenic according to our data. Variant chr14-74486324-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 8479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-74486324-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPC2 | NM_006432.5 | c.190+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000555619.6 | NP_006423.1 | |||
NPC2 | NM_001363688.1 | c.190+5G>A | splice_donor_5th_base_variant, intron_variant | NP_001350617.1 | ||||
NPC2 | NM_001375440.1 | c.190+5G>A | splice_donor_5th_base_variant, intron_variant | NP_001362369.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPC2 | ENST00000555619.6 | c.190+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | NM_006432.5 | ENSP00000451112 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000434 AC: 9AN: 207150Hom.: 0 AF XY: 0.0000182 AC XY: 2AN XY: 109940
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GnomAD4 exome AF: 0.0000196 AC: 28AN: 1431022Hom.: 0 Cov.: 31 AF XY: 0.0000212 AC XY: 15AN XY: 708608
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74486
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:6Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Niemann-Pick disease, type C2 Pathogenic:6Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | This sequence change falls in intron 2 of the NPC2 gene. It does not directly change the encoded amino acid sequence of the NPC2 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs80358268, gnomAD 0.01%). This variant has been observed in individuals with Niemann-Pick type C disease (PMID: 11567215, 28105569). This variant is also known as IVS2+5G>A. ClinVar contains an entry for this variant (Variation ID: 8479). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in abnormal RNA spliceforms and introduces a premature termination codon (PMID: 11567215). The resulting mRNA is expected to undergo nonsense-mediated decay. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2001 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Sep 01, 2017 | This variant has been previously reported as disease-causing and was found once in our laboratory homozygous in a 14-year-old male with intellectual disability, epilepsy, similarly affected sibling - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 16, 2021 | - - |
Likely pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 08, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Sep 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
Splicing
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at