rs786204564

chr18-23538609-CCT-C

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_000271.5(NPC1):c.2972_2973del(p.Gln991ArgfsTer15) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,068 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. Q991Q) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000029 (0 hom.)
• Consequence: NPC1 NM_000271.5 frameshift
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:9 U:1
• Conservation: PhyloP100: 1.47

Genes affected

NPC1 (HGNC:7897): (NPC intracellular cholesterol transporter 1) This gene encodes a large protein that resides in the limiting membrane of endosomes and lysosomes and mediates intracellular cholesterol trafficking via binding of cholesterol to its N-terminal domain. It is predicted to have a cytoplasmic C-terminus, 13 transmembrane domains, and 3 large loops in the lumen of the endosome - the last loop being at the N-terminus. This protein transports low-density lipoproteins to late endosomal/lysosomal compartments where they are hydrolized and released as free cholesterol. Defects in this gene cause Niemann-Pick type C disease, a rare autosomal recessive neurodegenerative disorder characterized by over accumulation of cholesterol and glycosphingolipids in late endosomal/lysosomal compartments.[provided by RefSeq, Aug 2009]

ACMG classification

Verdict is Pathogenic. Variant got 11 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 18-23538609-CCT-C is Pathogenic according to our data. Variant chr18-23538609-CCT-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 188932.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=7, Likely_pathogenic=1, Uncertain_significance=1}. Variant chr18-23538609-CCT-C is described in Lovd as [Pathogenic]. Variant chr18-23538609-CCT-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPC1	NM_000271.5	c.2972_2973del	p.Gln991ArgfsTer15	frameshift_variant	20/25	ENST00000269228.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPC1	ENST00000269228.10	c.2972_2973del	p.Gln991ArgfsTer15	frameshift_variant	20/25	1	NM_000271.5	P1
NPC1	ENST00000591051.1	c.2050_2051del	p.Gln684ArgfsTer15	frameshift_variant	13/18	2
NPC1	ENST00000591075.1	n.605_606del		non_coding_transcript_exon_variant	2/3	4
NPC1	ENST00000591955.1	n.315_316del		non_coding_transcript_exon_variant	1/2	4

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152200 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000477 AC: 12 AN: 251484 Hom.: 0 AF XY: 0.0000294 AC XY: 4 AN XY: 135916

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.0000992

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000653

Gnomad FIN exome AF: 0.0000924

Gnomad NFE exome AF: 0.0000527

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000294 AC: 43 AN: 1461868 Hom.: 0 AF XY: 0.0000248 AC XY: 18 AN XY: 727230

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.000191

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000464

Gnomad4 FIN exome AF: 0.0000749

Gnomad4 NFE exome AF: 0.0000207

Gnomad4 OTH exome AF: 0.0000662

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152200 Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1 AN XY: 74372

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.0000227

EpiCase AF: 0.0000545

EpiControl AF: 0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:9 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Niemann-Pick disease, type C1 Pathogenic:4

Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Jun 22, 2021	- -
Likely pathogenic, criteria provided, single submitter	literature only	Counsyl	Aug 21, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 19, 2018	The NPC1 c.2972_2973delAG (p.Gln991ArgfsTer15) variant has been reported in at least seven studies and is found in at least seven patients with suspected Neimann-Pick disease type C, including one in a homozygous state, five in a compound heterozygous state, and two in a heterozygous state where a second variant was not identified (Greer et al. 1999; Tarugi et al. 2002; Park et al. 2003; Fancello et al. 2009; Schicks et al. 2013; Zhang et al. 2014; Imrie et al. 2015). The p.Gln991ArgfsTer15 variant was absent from 250 controls but is reported at a frequency of 0.00006 in the European (non-Finnish) population of the Genome Aggregation Database. Data from Tarugi et al. (2002) suggest the allele carrying p.Gln991ArgfsTer15 is not transcribed or mRNA is rapidly degraded making it non-functional, as the allele was not identified using reverse transcription of RNA in fibroblasts of two unrelated compound heterozygous patients. Based on the evidence and the potential impact of frameshift variants, the p.Gln991ArgfsTer15 variant is classified as pathogenic for Niemann-Pick disease type C. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 25, 2024	This sequence change creates a premature translational stop signal (p.Gln991Argfs*15) in the NPC1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPC1 are known to be pathogenic (PMID: 9211850). This variant is present in population databases (rs756815030, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with Niemann-Pick disease type C (PMID: 12401890, 16126423, 23427322, 24915861, 26666848). This variant is also known as 2972del2. ClinVar contains an entry for this variant (Variation ID: 188932). For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:2 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 13, 2022	Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23427322, 16126423, 12955717, 10521290, 26666848, 16086131, 12401890, 24915861, 26790753, 32138288) -

Niemann-Pick disease, type C Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 19, 2018	Variant summary: NPC1 c.2972_2973delAG (p.Gln991ArgfsX15) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (e.g. c.3742_3745delCTCA (p.Leu1248fsX3)). The variant allele was found at a frequency of 4.7e-05 in 277230 control chromosomes. This frequency is not higher than expected for a pathogenic variant in NPC1 causing Niemann-Pick Disease Type C (4.7e-05 vs 0.0028), allowing no conclusion about variant significance. c.2972_2973delAG has been reported in the literature in multiple individuals affected with Niemann-Pick Disease Type C, including several homozygous patients who are severely affected (e.g. Millat_2005, Fancello_2009, Elmonem_2016). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 09, 2020	The p.Gln991ArgfsX15 variant in NPC1 has been reported in at least 8 individuals with Neimann-Pick Type C, in the compound heterozygous (5), homozygous (2) or heterozygous state (1) (Greer 1999 PMID: 10521290, Tarugi 2002 PMID: 12401890, Palmeri 2005 PMID: 16086131, Millat 2005 PMID: 16126423, Schicks 2013 PMID: 23427322, Imrie 2015 PMID: 26666848, Elmonem 2016 PMID: 26830282). It has also been identified in 0.01% (2/30616) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). However, this frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID 188932). This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 991 and leads to a premature termination codon 15 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the NPC1 gene is an established disease mechanism in autosomal recessive Niemann-Pick Type C Disease. In vitro functional studies provide some evidence that this variant does impacts protein function (Tarugi 2002 PMID: 12401890); however, these types of assays may not accurately represent biological function. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Niemann-Pick Type C Disease. ACMG/AMP Criteria applied: PVS1, PM3_Strong, PM2_Supporting, PS3_Supporting. -

NPC1-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

May 19, 2023

The NPC1 c.2972_2973delAG variant is predicted to result in a frameshift and premature protein termination (p.Gln991Argfs*15). This variant has been reported in individuals with Niemann-Pick type C (Tarugi et al. 2002. PubMed ID: 12401890; Millat et al. 2005. PubMed ID: 16126423; Schicks et al. 2013. PubMed ID: 23427322; Zhang et al. 2014. PubMed ID: 24915861; Imrie et al. 2015. PubMed ID: 26666848). This variant is reported in 0.0096% of alleles in individuals of Ashkenazi Jewish descent in gnomAD (http://gnomad.broadinstitute.org/variant/18-21118573-CCT-C). Frameshift variants in NPC1 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs756815030; hg19: chr18-21118573;