rs1555066796
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM4PP5
The NM_001080463.2(DYNC2H1):c.7774_7782del(p.Leu2592_Pro2594del) variant causes a inframe deletion change. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. P2591P) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
DYNC2H1
NM_001080463.2 inframe_deletion
NM_001080463.2 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.83
Genes affected
DYNC2H1 (HGNC:2962): (dynein cytoplasmic 2 heavy chain 1) This gene encodes a large cytoplasmic dynein protein that is involved in retrograde transport in the cilium and has a role in intraflagellar transport, a process required for ciliary/flagellar assembly. Mutations in this gene cause a heterogeneous spectrum of conditions related to altered primary cilium function and often involve polydactyly, abnormal skeletogenesis, and polycystic kidneys. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_001080463.2.
PP5
?
Variant 11-103197994-ACCATTACCT-A is Pathogenic according to our data. Variant chr11-103197994-ACCATTACCT-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 446538.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.7774_7782del | p.Leu2592_Pro2594del | inframe_deletion | 48/90 | ENST00000650373.2 | |
DYNC2H1 | NM_001377.3 | c.7774_7782del | p.Leu2592_Pro2594del | inframe_deletion | 48/89 | ENST00000375735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000375735.7 | c.7774_7782del | p.Leu2592_Pro2594del | inframe_deletion | 48/89 | 1 | NM_001377.3 | P3 | |
DYNC2H1 | ENST00000650373.2 | c.7774_7782del | p.Leu2592_Pro2594del | inframe_deletion | 48/90 | NM_001080463.2 | A1 | ||
DYNC2H1 | ENST00000334267.11 | c.2205+63579_2205+63587del | intron_variant | 1 | |||||
DYNC2H1 | ENST00000649323.1 | c.*5298_*5306del | 3_prime_UTR_variant, NMD_transcript_variant | 46/51 |
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/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Asphyxiating thoracic dystrophy 3 Pathogenic:2
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Pathogenic, no assertion criteria provided | research | Dan Cohn Lab, University Of California Los Angeles | Jun 01, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at