11-94129365-AGGAGCCCAC-A

Variant names:

• chr11-94129365-AGGAGCCCAC-A
• rs1591499598
• NM_015368.4:c.62_70delCGGAGCCCA

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PM4 PP5

The NM_015368.4(PANX1):​c.62_70delCGGAGCCCA​(p.Thr21_Pro23del) variant causes a disruptive 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 disruptive_inframe_deletion
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• 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]

ACMG classification

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 rank	MANE	Protein	UniProt
PANX1	NM_015368.4	c.62_70delCGGAGCCCA	p.Thr21_Pro23del	disruptive_inframe_deletion	Exon 1 of 5	ENST00000227638.8	NP_056183.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PANX1	ENST00000227638.8	c.62_70delCGGAGCCCA	p.Thr21_Pro23del	disruptive_inframe_deletion	Exon 1 of 5	1	NM_015368.4	ENSP00000227638.3
PANX1	ENST00000436171.2	c.62_70delCGGAGCCCA	p.Thr21_Pro23del	disruptive_inframe_deletion	Exon 1 of 5	1		ENSP00000411461.2

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Oocyte maturation defect 7 Pathogenic:1

Apr 10, 2023

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1591499598; hg19: chr11-93862531;