NM_194318.4:c.71-9_71-5delTTTTT

Variant names:

• chr13-31215032-CTTTTT-C
• NM_194318.4:c.71-9_71-5delTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_194318.4(B3GLCT):​c.71-9_71-5delTTTTT 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 1,110,204 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GLCT	NM_194318.4	c.71-9_71-5delTTTTT		splice_region_variant, intron_variant	Intron 1 of 14	ENST00000343307.5	NP_919299.3
B3GLCT	XM_006719768.4	c.14-9_14-5delTTTTT		splice_region_variant, intron_variant	Intron 1 of 14		XP_006719831.1
B3GLCT	XM_011534936.2	c.71-9_71-5delTTTTT		splice_region_variant, intron_variant	Intron 1 of 13		XP_011533238.1
B3GLCT	XM_047430111.1	c.71-9_71-5delTTTTT		splice_region_variant, intron_variant	Intron 1 of 11		XP_047286067.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5	c.71-18_71-14delTTTTT		intron_variant	Intron 1 of 14	1	NM_194318.4	ENSP00000343002.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 9.01e-7 AC: 1 AN: 1110204 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 556990

Gnomad4 AFR exome AF: 0.0000375

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

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: chr13-31789169;