4-625794-C-CACGGCGCTGCTGGAGCTGGTGCAGGATATGCAGGAGAGCATCAACATGGAGCGCGTGGTCTTCAAGGTCCT

Position:

• chr4-625794-C-CACGGCGCTGCTGGAGCTGGTGCAGGATATGCAGGAGAGCATCAACATGGAGCGCGTGGTCTTCAAGGTCCT

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000283.4(PDE6B):​c.169_239dupACGGCGCTGCTGGAGCTGGTGCAGGATATGCAGGAGAGCATCAACATGGAGCGCGTGGTCTTCAAGGTCCT​(p.Leu83fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,012 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: PDE6B NM_000283.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: -0.0170

Genes affected

PDE6B (HGNC:8786): (phosphodiesterase 6B) Photon absorption triggers a signaling cascade in rod photoreceptors that activates cGMP phosphodiesterase (PDE), resulting in the rapid hydrolysis of cGMP, closure of cGMP-gated cation channels, and hyperpolarization of the cell. PDE is a peripheral membrane heterotrimeric enzyme made up of alpha, beta, and gamma subunits. This gene encodes the beta subunit. Mutations in this gene result in retinitis pigmentosa and autosomal dominant congenital stationary night blindness. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 4-625794-C-CACGGCGCTGCTGGAGCTGGTGCAGGATATGCAGGAGAGCATCAACATGGAGCGCGTGGTCTTCAAGGTCCT is Pathogenic according to our data. Variant chr4-625794-C-CACGGCGCTGCTGGAGCTGGTGCAGGATATGCAGGAGAGCATCAACATGGAGCGCGTGGTCTTCAAGGTCCT is described in ClinVar as [Pathogenic]. Clinvar id is 13108.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE6B	NM_000283.4	c.169_239dupACGGCGCTGCTGGAGCTGGTGCAGGATATGCAGGAGAGCATCAACATGGAGCGCGTGGTCTTCAAGGTCCT	p.Leu83fs	frameshift_variant	1/22	ENST00000496514.6	NP_000274.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE6B	ENST00000496514.6	c.169_239dupACGGCGCTGCTGGAGCTGGTGCAGGATATGCAGGAGAGCATCAACATGGAGCGCGTGGTCTTCAAGGTCCT	p.Leu83fs	frameshift_variant	1/22	1	NM_000283.4	ENSP00000420295.1
PDE6B	ENST00000255622.10	c.169_239dupACGGCGCTGCTGGAGCTGGTGCAGGATATGCAGGAGAGCATCAACATGGAGCGCGTGGTCTTCAAGGTCCT	p.Leu83fs	frameshift_variant	1/22	1		ENSP00000255622.6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461012 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 726854

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 20, 2023

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 13108). This premature translational stop signal has been observed in individual(s) with retinitis pigmentosa (PMID: 7599633). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu83Cysfs*91) in the PDE6B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PDE6B are known to be pathogenic (PMID: 8394174, 8595886, 22334370). -

Retinitis pigmentosa 40 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 1995

- -

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: rs1553801591; hg19: chr4-619583;