NM_001371596.2:c.754+2T>A
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001371596.2(MFSD8):c.754+2T>A variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.0000162 in 1,606,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_001371596.2 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MFSD8 | NM_001371596.2 | c.754+2T>A | splice_donor_variant, intron_variant | Intron 7 of 11 | ENST00000641686.2 | NP_001358525.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151996Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250734Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135588
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1454646Hom.: 0 Cov.: 28 AF XY: 0.0000207 AC XY: 15AN XY: 724082
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151996Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74262
ClinVar
Submissions by phenotype
Neuronal ceroid lipofuscinosis 7 Pathogenic:4
This sequence change affects a donor splice site in intron 8 of the MFSD8 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MFSD8 are known to be pathogenic (PMID: 19177532, 25227500, 28586915). This variant is present in population databases (rs587778809, gnomAD 0.003%). Disruption of this splice site has been observed in individuals with MFSD8-related conditions (PMID: 17564970, 19201763, 25439737). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 65897). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2,PP3,PP5. -
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The MFSD8 c.754+2T>A variant occurs in a canonical splice donor site and is therefore predicted to disrupt or distort the normal gene product. The variant has been reported in four studies and found in a total of 12 individuals with confirmed or suspected neuronal ceroid-lipofuscinosis, including in eight individuals (including two siblings) in a homozygous state and in four individuals in a compound heterozygous state (Siintola et al. 2007; Kousi et al. 2009; Kousi et al. 2011; Craiu et al. 2015). The c.754+2T>A variant was also reported in a heterozygous state in one unaffected parent. The variant was absent from 504 control chromosomes and not found in the 1000 Genomes Project, the Exome Sequencing Project, or the Exome Aggregation Consortium. RT-PCR showed aberrant splicing of the variant mRNA leading to an altered pattern of products including almost complete loss of the normal transcript containing exons 7-10 of the gene (Siintola et al. 2007). Based on potential impact of splice donor variants and the evidence from the literature, the c.754+2T>A variant is classified as pathogenic for neuronal ceroid-lipofuscinosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Macular dystrophy with central cone involvement Pathogenic:1
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Late-infantile neuronal ceroid lipofuscinosis Pathogenic:1
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not provided Pathogenic:1
Canonical splice site variant predicted to result in a null allele 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); A different variant affecting the same splice site (c.754+1G>A) has been reported in association with late infantile neuronal ceroid lipofuscinosis (Kousi et al., 2012); This variant is associated with the following publications: (PMID: 25525159, 19277732, 25439737, 31589614, 17564970) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at