13-31200145-T-C

Variant names:

• chr13-31200145-T-C
• rs1478988254
• NM_194318.4:c.61T>C

Variant summary

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

The NM_194318.4(B3GLCT):​c.61T>C​(p.Cys21Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: B3GLCT NM_194318.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

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.61T>C	p.Cys21Arg	missense_variant	Exon 1 of 15	ENST00000343307.5	NP_919299.3
B3GLCT	XM_011534936.2	c.61T>C	p.Cys21Arg	missense_variant	Exon 1 of 14		XP_011533238.1
B3GLCT	XM_047430111.1	c.61T>C	p.Cys21Arg	missense_variant	Exon 1 of 12		XP_047286067.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GLCT	ENST00000343307.5	c.61T>C	p.Cys21Arg	missense_variant	Exon 1 of 15	1	NM_194318.4	ENSP00000343002.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1205548 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 593052

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Uncertain	0.068	T
BayesDel_noAF	Benign	-0.14
CADD	Benign	18
DANN	Benign	0.94
DEOGEN2	Benign	0.072	T
Eigen	Benign	-0.033
Eigen_PC	Benign	-0.11
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.33	T
M_CAP	Pathogenic	0.29	D
MetaRNN	Uncertain	0.45	T
MetaSVM	Benign	-0.61	T
MutationAssessor	Benign	0.67	N
PrimateAI	Uncertain	0.62	T
PROVEAN	Benign	-2.0	N
REVEL	Uncertain	0.46
Sift	Uncertain	0.0060	D
Sift4G	Benign	0.39	T
Polyphen		0.94	P
Vest4		0.28
MutPred		0.71		Gain of disorder (P = 0.0607);
MVP		0.78
MPC		0.38
ClinPred		0.30	T
GERP RS		2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
Varity_R		0.53
gMVP		0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1478988254; hg19: chr13-31774282;