NM_000283.4:c.718C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000283.4(PDE6B):c.718C>T(p.Leu240Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
PDE6B
NM_000283.4 synonymous
NM_000283.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.884
Publications
0 publications found
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BP6
Variant 4-653858-C-T is Benign according to our data. Variant chr4-653858-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2128085.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.884 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000283.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDE6B | MANE Select | c.718C>T | p.Leu240Leu | synonymous | Exon 4 of 22 | NP_000274.3 | P35913-1 | ||
| PDE6B | c.-120C>T | 5_prime_UTR_premature_start_codon_gain | Exon 2 of 20 | NP_001337083.1 | |||||
| PDE6B | c.-120C>T | 5_prime_UTR_premature_start_codon_gain | Exon 2 of 20 | NP_001138764.2 | P35913-3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDE6B | TSL:1 MANE Select | c.718C>T | p.Leu240Leu | synonymous | Exon 4 of 22 | ENSP00000420295.1 | P35913-1 | ||
| PDE6B | TSL:1 | c.718C>T | p.Leu240Leu | synonymous | Exon 4 of 22 | ENSP00000255622.6 | P35913-2 | ||
| PDE6B | TSL:1 | n.116C>T | non_coding_transcript_exon | Exon 2 of 3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461290Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726954 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461290
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
726954
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
1
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
52858
Middle Eastern (MID)
AF:
AC:
0
AN:
5764
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111982
Other (OTH)
AF:
AC:
0
AN:
60390
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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