rs759505367
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_194318.4(B3GLCT):c.101_104delAAGA(p.Lys34ArgfsTer19) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,456,810 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: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
B3GLCT
NM_194318.4 frameshift
NM_194318.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.90
Publications
0 publications found
Genes affected
B3GLCT (HGNC:20207): (beta 3-glucosyltransferase) The protein encoded by this gene is a beta-1,3-glucosyltransferase that transfers glucose to O-linked fucosylglycans on thrombospondin type-1 repeats (TSRs) of several proteins. The encoded protein is a type II membrane protein. Defects in this gene are a cause of Peters-plus syndrome (PPS).[provided by RefSeq, Mar 2009]
B3GLCT Gene-Disease associations (from GenCC):
- Peters plus syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet, G2P, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 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 13-31215075-CAAAG-C is Pathogenic according to our data. Variant chr13-31215075-CAAAG-C is described in ClinVar as Pathogenic. ClinVar VariationId is 1324051.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_194318.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| B3GLCT | NM_194318.4 | MANE Select | c.101_104delAAGA | p.Lys34ArgfsTer19 | frameshift | Exon 2 of 15 | NP_919299.3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| B3GLCT | ENST00000343307.5 | TSL:1 MANE Select | c.101_104delAAGA | p.Lys34ArgfsTer19 | frameshift | Exon 2 of 15 | ENSP00000343002.4 | Q6Y288 | |
| B3GLCT | ENST00000873566.1 | c.101_104delAAGA | p.Lys34ArgfsTer19 | frameshift | Exon 2 of 13 | ENSP00000543625.1 | |||
| B3GLCT | ENST00000946543.1 | c.101_104delAAGA | p.Lys34ArgfsTer21 | frameshift | Exon 2 of 11 | ENSP00000616602.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000802 AC: 2AN: 249374 AF XY: 0.0000148 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
249374
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1456810Hom.: 0 AF XY: 0.00000276 AC XY: 2AN XY: 724778 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1456810
Hom.:
AF XY:
AC XY:
2
AN XY:
724778
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33392
American (AMR)
AF:
AC:
0
AN:
44572
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26072
East Asian (EAS)
AF:
AC:
0
AN:
39606
South Asian (SAS)
AF:
AC:
0
AN:
85756
European-Finnish (FIN)
AF:
AC:
0
AN:
50952
Middle Eastern (MID)
AF:
AC:
0
AN:
5742
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1110452
Other (OTH)
AF:
AC:
0
AN:
60266
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
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2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Pathogenic
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
1
-
-
Peters plus syndrome (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
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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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