chr15-82851190-CTGAGG-C
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_004839.4(HOMER2):c.799_803del(p.Pro267AlafsTer10) variant causes a frameshift 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 (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
HOMER2
NM_004839.4 frameshift
NM_004839.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.75
Genes affected
HOMER2 (HGNC:17513): (homer scaffold protein 2) This gene encodes a member of the homer family of dendritic proteins. Members of this family regulate group 1 metabotrophic glutamate receptor function. The encoded protein is a postsynaptic density scaffolding protein. Alternative splicing results in multiple transcript variants. Two related pseudogenes have been identified on chromosome 14. [provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.226 CDS is truncated, and there are 2 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 15-82851190-CTGAGG-C is Pathogenic according to our data. Variant chr15-82851190-CTGAGG-C is described in ClinVar as [Pathogenic]. Clinvar id is 1013607.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOMER2 | NM_004839.4 | c.799_803del | p.Pro267AlafsTer10 | frameshift_variant | 8/9 | ENST00000450735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOMER2 | ENST00000450735.7 | c.799_803del | p.Pro267AlafsTer10 | frameshift_variant | 8/9 | 1 | NM_004839.4 | ||
HOMER2 | ENST00000304231.12 | c.832_836del | p.Pro278AlafsTer10 | frameshift_variant | 8/9 | 5 | P1 | ||
HOMER2 | ENST00000558552.1 | n.679_683del | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
HOMER2 | ENST00000558817.1 | downstream_gene_variant | 3 |
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
Autosomal dominant nonsyndromic hearing loss 68 Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Genetics Department, Hospital Ramon y Cajal-IRYCIS | Mar 07, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at