NM_194318.4:c.32C>T

Variant names:

• chr13-31200116-C-T
• rs1868555417
• NM_194318.4:c.32C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_194318.4(B3GLCT):​c.32C>T​(p.Ala11Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000218 in 1,376,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A11E) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000067 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: B3GLCT NM_194318.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• 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: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.097212225).

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.32C>T	p.Ala11Val	missense	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.32C>T	p.Ala11Val	missense	Exon 1 of 15	ENSP00000343002.4	Q6Y288
	B3GLCT	ENST00000873566.1		c.32C>T	p.Ala11Val	missense	Exon 1 of 13	ENSP00000543625.1
	B3GLCT	ENST00000946543.1		c.32C>T	p.Ala11Val	missense	Exon 1 of 11	ENSP00000616602.1

Frequencies

GnomAD3 genomes AF: 0.00000665 AC: 1 AN: 150334 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000485

GnomAD4 exome AF: 0.00000163 AC: 2 AN: 1225830 Hom.: 0 Cov.: 30 AF XY: 0.00000331 AC XY: 2 AN XY: 603906

African (AFR) AF: 0.00 AC: 0 AN: 24620

American (AMR) AF: 0.00 AC: 0 AN: 23478

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19824

East Asian (EAS) AF: 0.00 AC: 0 AN: 23184

South Asian (SAS) AF: 0.00 AC: 0 AN: 66674

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28660

Middle Eastern (MID) AF: 0.000587 AC: 2 AN: 3408

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 987942

Other (OTH) AF: 0.00 AC: 0 AN: 48040

GnomAD4 genome AF: 0.00000665 AC: 1 AN: 150334 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 73348

African (AFR) AF: 0.00 AC: 0 AN: 41266

American (AMR) AF: 0.00 AC: 0 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3446

East Asian (EAS) AF: 0.00 AC: 0 AN: 5154

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9936

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67302

Other (OTH) AF: 0.000485 AC: 1 AN: 2060

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.056	T
BayesDel_noAF	Benign	-0.32
CADD	Benign	14
DANN	Benign	0.97
DEOGEN2	Benign	0.041	T
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.80
FATHMM_MKL	Benign	0.040	N
LIST_S2	Benign	0.40	T
M_CAP	Benign	0.060	D
MetaRNN	Benign	0.097	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.0	N
PhyloP100		0.34
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	0.70	N
REVEL	Benign	0.088
Sift	Benign	0.55	T
Sift4G	Benign	0.56	T
Polyphen		0.60	P
Vest4		0.22
MutPred		0.32		Gain of sheet (P = 0.0125)
MVP		0.52
MPC		0.30
ClinPred		0.13	T
GERP RS		1.2
PromoterAI		0.050	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		3.0
Varity_R		0.045
gMVP		0.21
Mutation Taster		=93/7	polymorphism

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

Other links and lift over

dbSNP: rs1868555417; hg19: chr13-31774253;