11-94129365-AGGAGCCCAC-A
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The NM_015368.4(PANX1):c.62_70del(p.Thr21_Pro23del) 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).
Frequency
Genomes: not found (cov: 32)
Consequence
PANX1
NM_015368.4 inframe_deletion
NM_015368.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.36
Genes affected
PANX1 (HGNC:8599): (pannexin 1) The protein encoded by this gene belongs to the innexin family. Innexin family members are the structural components of gap junctions. This protein and pannexin 2 are abundantly expressed in central nerve system (CNS) and are coexpressed in various neuronal populations. Studies in Xenopus oocytes suggest that this protein alone and in combination with pannexin 2 may form cell type-specific gap junctions with distinct properties. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_015368.4.
PP5
?
Variant 11-94129365-AGGAGCCCAC-A is Pathogenic according to our data. Variant chr11-94129365-AGGAGCCCAC-A is described in ClinVar as [Pathogenic]. Clinvar id is 689424.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr11-94129365-AGGAGCCCAC-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PANX1 | NM_015368.4 | c.62_70del | p.Thr21_Pro23del | inframe_deletion | 1/5 | ENST00000227638.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PANX1 | ENST00000227638.8 | c.62_70del | p.Thr21_Pro23del | inframe_deletion | 1/5 | 1 | NM_015368.4 | P3 | |
PANX1 | ENST00000436171.2 | c.62_70del | p.Thr21_Pro23del | inframe_deletion | 1/5 | 1 | A1 |
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
Oocyte maturation defect 7 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 10, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at