13-31200107-GGCTGCTCGCGCCGCCGGC-GGCTGCTCGCGCCGCCGGCGCTGCTCGCGCCGCCGGC

Variant names:

• chr13-31200107-G-GGCTGCTCGCGCCGCCGGC
• rs777497613
• NM_194318.4:c.35_52dupCGCCGGCGCTGCTCGCGC

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM4

The NM_194318.4(B3GLCT):​c.35_52dupCGCCGGCGCTGCTCGCGC​(p.Pro12_Ala17dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000245 in 1,225,234 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000024 (0 hom.)
• Consequence: B3GLCT NM_194318.4 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• 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: PanelApp Australia, Orphanet, G2P, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• PM4: Nonframeshift variant in NON repetitive region in NM_194318.4.

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.35_52dupCGCCGGCGCTGCTCGCGC	p.Pro12_Ala17dup	disruptive_inframe_insertion	Exon 1 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.35_52dupCGCCGGCGCTGCTCGCGC	p.Pro12_Ala17dup	disruptive_inframe_insertion	Exon 1 of 15	ENSP00000343002.4	Q6Y288
	B3GLCT	ENST00000873566.1		c.35_52dupCGCCGGCGCTGCTCGCGC	p.Pro12_Ala17dup	disruptive_inframe_insertion	Exon 1 of 13	ENSP00000543625.1
	B3GLCT	ENST00000946543.1		c.35_52dupCGCCGGCGCTGCTCGCGC	p.Pro12_Ala17dup	disruptive_inframe_insertion	Exon 1 of 11	ENSP00000616602.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000245 AC: 3 AN: 1225234 Hom.: 0 Cov.: 30 AF XY: 0.00000331 AC XY: 2 AN XY: 603530

African (AFR) AF: 0.00 AC: 0 AN: 24654

American (AMR) AF: 0.00 AC: 0 AN: 23574

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19868

East Asian (EAS) AF: 0.00 AC: 0 AN: 23302

South Asian (SAS) AF: 0.00 AC: 0 AN: 66356

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28496

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3410

European-Non Finnish (NFE) AF: 0.00000101 AC: 1 AN: 987558

Other (OTH) AF: 0.0000417 AC: 2 AN: 48016

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs777497613; hg19: chr13-31774244;