rs876661302
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP3PP5BP3
The NM_002473.6(MYH9):c.3195_3215del(p.Gln1068_Leu1074del) variant causes a inframe deletion 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). Synonymous variant affecting the same amino acid position (i.e. A1065A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
MYH9
NM_002473.6 inframe_deletion
NM_002473.6 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.97
Genes affected
MYH9 (HGNC:7579): (myosin heavy chain 9) This gene encodes a conventional non-muscle myosin; this protein should not be confused with the unconventional myosin-9a or 9b (MYO9A or MYO9B). The encoded protein is a myosin IIA heavy chain that contains an IQ domain and a myosin head-like domain which is involved in several important functions, including cytokinesis, cell motility and maintenance of cell shape. Defects in this gene have been associated with non-syndromic sensorineural deafness autosomal dominant type 17, Epstein syndrome, Alport syndrome with macrothrombocytopenia, Sebastian syndrome, Fechtner syndrome and macrothrombocytopenia with progressive sensorineural deafness. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
?
Variant 22-36296899-CGCGATCTGGGCCTGGAGCTCG-C is Pathogenic according to our data. Variant chr22-36296899-CGCGATCTGGGCCTGGAGCTCG-C is described in ClinVar as [Pathogenic]. Clinvar id is 14084.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr22-36296899-CGCGATCTGGGCCTGGAGCTCG-C is described in Lovd as [Pathogenic]. Variant chr22-36296899-CGCGATCTGGGCCTGGAGCTCG-C is described in Lovd as [Pathogenic].
BP3
?
Nonframeshift variant in repetitive region in NM_002473.6
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH9 | NM_002473.6 | c.3195_3215del | p.Gln1068_Leu1074del | inframe_deletion | 25/41 | ENST00000216181.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH9 | ENST00000216181.11 | c.3195_3215del | p.Gln1068_Leu1074del | inframe_deletion | 25/41 | 1 | NM_002473.6 | P1 | |
MYH9 | ENST00000685801.1 | c.3258_3278del | p.Gln1089_Leu1095del | inframe_deletion | 26/42 | ||||
MYH9 | ENST00000459960.1 | n.404_424del | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
MYH9 | ENST00000691109.1 | n.3490_3510del | non_coding_transcript_exon_variant | 19/35 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2009 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at