13-31215032-CTTTTTT-CTTTTTTTT

Variant names:

• chr13-31215032-C-CTT
• rs398022187
• NM_194318.4:c.71-6_71-5dupTT

Variant summary

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

The NM_194318.4(B3GLCT):​c.71-6_71-5dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000099 (0 hom.)
• Consequence: B3GLCT NM_194318.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• 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 syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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.71-6_71-5dupTT		splice_region intron	N/A	NP_919299.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GLCT	ENST00000343307.5	TSL:1 MANE Select	c.71-19_71-18insTT		intron	N/A	ENSP00000343002.4	Q6Y288
	B3GLCT	ENST00000873566.1		c.71-19_71-18insTT		intron	N/A	ENSP00000543625.1
	B3GLCT	ENST00000946543.1		c.71-19_71-18insTT		intron	N/A	ENSP00000616602.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000991 AC: 11 AN: 1109966 Hom.: 0 Cov.: 0 AF XY: 0.00000180 AC XY: 1 AN XY: 556870

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000376 AC: 1 AN: 26626

American (AMR) AF: 0.00 AC: 0 AN: 34656

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20846

East Asian (EAS) AF: 0.00 AC: 0 AN: 32284

South Asian (SAS) AF: 0.00 AC: 0 AN: 67244

European-Finnish (FIN) AF: 0.0000544 AC: 2 AN: 36738

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4484

European-Non Finnish (NFE) AF: 0.00000714 AC: 6 AN: 840412

Other (OTH) AF: 0.0000428 AC: 2 AN: 46676

⚠️ 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.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs398022187; hg19: chr13-31789169;