GeneBe

rs398022187

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_194318.4(B3GLCT):​c.71-10_71-5delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000901 in 1,110,254 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 9.0e-7 ( 0 hom. )

Consequence

B3GLCT
NM_194318.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.775

Publications

0 publications found
Variant links:
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 syndrome
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

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.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
B3GLCT
NM_194318.4
MANE Select
c.71-10_71-5delTTTTTT
splice_region intron
N/ANP_919299.3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
B3GLCT
ENST00000343307.5
TSL:1 MANE Select
c.71-18_71-13delTTTTTT
intron
N/AENSP00000343002.4Q6Y288
B3GLCT
ENST00000873566.1
c.71-18_71-13delTTTTTT
intron
N/AENSP00000543625.1
B3GLCT
ENST00000946543.1
c.71-18_71-13delTTTTTT
intron
N/AENSP00000616602.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
9.01e-7
AC:
1
AN:
1110254
Hom.:
0
AF XY:
0.00000180
AC XY:
1
AN XY:
557008
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
26636
American (AMR)
AF:
0.00
AC:
0
AN:
34660
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20846
East Asian (EAS)
AF:
0.00
AC:
0
AN:
32286
South Asian (SAS)
AF:
0.00
AC:
0
AN:
67262
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
36740
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4484
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
840654
Other (OTH)
AF:
0.0000214
AC:
1
AN:
46686
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
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
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.78
Mutation Taster
=100/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs398022187; hg19: chr13-31789169; API