13-31200107-GGCTGCTCGCGCCGCCGGC-GGCTGCTCGCGCCGCCGGCGCTGCTCGCGCCGCCGGC

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 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. 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

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_194318.4.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GLCT	NM_194318.4	c.35_52dupCGCCGGCGCTGCTCGCGC	p.Pro12_Ala17dup	disruptive_inframe_insertion	Exon 1 of 15	ENST00000343307.5	NP_919299.3
B3GLCT	XM_011534936.2	c.35_52dupCGCCGGCGCTGCTCGCGC	p.Pro12_Ala17dup	disruptive_inframe_insertion	Exon 1 of 14		XP_011533238.1
B3GLCT	XM_047430111.1	c.35_52dupCGCCGGCGCTGCTCGCGC	p.Pro12_Ala17dup	disruptive_inframe_insertion	Exon 1 of 12		XP_047286067.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5	c.35_52dupCGCCGGCGCTGCTCGCGC	p.Pro12_Ala17dup	disruptive_inframe_insertion	Exon 1 of 15	1	NM_194318.4	ENSP00000343002.4

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000101

Gnomad4 OTH exome AF: 0.0000417

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr13-31774244;