rs864621965
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM4PP3PP5
The NM_000435.3(NOTCH3):c.714_758del(p.Asp239_Asp253del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. D238D) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Consequence
NOTCH3
NM_000435.3 inframe_deletion
NM_000435.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.25
Genes affected
NOTCH3 (HGNC:7883): (notch receptor 3) This gene encodes the third discovered human homologue of the Drosophilia melanogaster type I membrane protein notch. In Drosophilia, notch interaction with its cell-bound ligands (delta, serrate) establishes an intercellular signalling pathway that plays a key role in neural development. Homologues of the notch-ligands have also been identified in human, but precise interactions between these ligands and the human notch homologues remains to be determined. Mutations in NOTCH3 have been identified as the underlying cause of cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM1
?
In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 4 uncertain in NM_000435.3
PM4
?
Nonframeshift variant in NON repetitive region in NM_000435.3.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
?
Variant 19-15191788-ATCCACGCATGTCCCCCCATTGAGACATCGGTGTCCTGGACAGTCG-A is Pathogenic according to our data. Variant chr19-15191788-ATCCACGCATGTCCCCCCATTGAGACATCGGTGTCCTGGACAGTCG-A is described in ClinVar as [Pathogenic]. Clinvar id is 9222.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr19-15191788-ATCCACGCATGTCCCCCCATTGAGACATCGGTGTCCTGGACAGTCG-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOTCH3 | NM_000435.3 | c.714_758del | p.Asp239_Asp253del | inframe_deletion | 5/33 | ENST00000263388.7 | |
NOTCH3 | XM_005259924.5 | c.714_758del | p.Asp239_Asp253del | inframe_deletion | 5/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOTCH3 | ENST00000263388.7 | c.714_758del | p.Asp239_Asp253del | inframe_deletion | 5/33 | 1 | NM_000435.3 | P1 | |
NOTCH3 | ENST00000601011.1 | c.711_755del | p.Asp238_Asp252del | inframe_deletion | 5/23 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 13, 2001 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at