rs1553699115

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_014159.7(SETD2):​c.4457_4460del​(p.Lys1486ArgfsTer28) variant causes a frameshift, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 31)

Consequence

SETD2
NM_014159.7 frameshift, splice_region

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:2

Conservation

PhyloP100: 7.99
Variant links:
Genes affected
SETD2 (HGNC:18420): (SET domain containing 2, histone lysine methyltransferase) Huntington's disease (HD), a neurodegenerative disorder characterized by loss of striatal neurons, is caused by an expansion of a polyglutamine tract in the HD protein huntingtin. This gene encodes a protein belonging to a class of huntingtin interacting proteins characterized by WW motifs. This protein is a histone methyltransferase that is specific for lysine-36 of histone H3, and methylation of this residue is associated with active chromatin. This protein also contains a novel transcriptional activation domain and has been found associated with hyperphosphorylated RNA polymerase II. [provided by RefSeq, Aug 2008]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 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 3-47116748-CTTCT-C is Pathogenic according to our data. Variant chr3-47116748-CTTCT-C is described in ClinVar as [Pathogenic]. Clinvar id is 521901.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SETD2NM_014159.7 linkuse as main transcriptc.4457_4460del p.Lys1486ArgfsTer28 frameshift_variant, splice_region_variant 4/21 ENST00000409792.4 NP_054878.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SETD2ENST00000409792.4 linkuse as main transcriptc.4457_4460del p.Lys1486ArgfsTer28 frameshift_variant, splice_region_variant 4/215 NM_014159.7 ENSP00000386759 P3Q9BYW2-1

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsJul 14, 2017Lines of evidence used in support of classification: POSITIVE: Relevant Alteration(s) Detected -
not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingGeneDxAug 15, 2023Frameshift 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 in large population cohorts (gnomAD); Previously reported as a de novo variant with confirmed parentage in patient with severe developmental delay; this individual was also identified with missense variants in other genes (Mcrae et al., 2017); This variant is associated with the following publications: (PMID: 24852293, 26084711, 31785789, 28424246, 27317772, 25574603, 24267886, 23160955, 22495309, 24901346, 28191890, 28135719) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.47
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.47
Position offset: -1

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1553699115; hg19: chr3-47158238; API