B3GNT4 p.Phe157Leu

Variant names:

• chr12-122206722-C-A
• NM_030765.4:c.471C>A
• B3GNT4 p.Phe157Leu

Your query was ambiguous. Multiple possible variants found:

• chr12-122206722-C-A
• chr12-122206722-C-G
• chr12-122206720-T-C
• chr12-122206720-TTC-CTT
• chr12-122206720-TTC-CTA
• chr12-122206720-TTC-CTG

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_030765.4(B3GNT4):​c.471C>A​(p.Phe157Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: B3GNT4 NM_030765.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 0 publications found

Genes affected

B3GNT4 (HGNC:15683): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase protein family. The encoded enzyme is involved in the biosynthesis of poly-N-acetyllactosamine chains and prefers lacto-N-neotetraose as a substrate. It is a type II transmembrane protein. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.902

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030765.4. 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
	B3GNT4	NM_030765.4	MANE Select	c.471C>A	p.Phe157Leu	missense	Exon 3 of 3	NP_110392.1	Q9C0J1-1
	B3GNT4	NM_001330492.2		c.396C>A	p.Phe132Leu	missense	Exon 2 of 2	NP_001317421.1	Q9C0J1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GNT4	ENST00000324189.5	TSL:1 MANE Select	c.471C>A	p.Phe157Leu	missense	Exon 3 of 3	ENSP00000319636.4	Q9C0J1-1
	B3GNT4	ENST00000535274.1	TSL:6	c.396C>A	p.Phe132Leu	missense	Exon 1 of 1	ENSP00000444534.1	Q9C0J1-2
	B3GNT4	ENST00000546192.1	TSL:2	c.396C>A	p.Phe132Leu	missense	Exon 2 of 2	ENSP00000438840.1	Q9C0J1-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.34	T
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.24
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.78	T
M_CAP	Benign	0.076	D
MetaRNN	Pathogenic	0.90	D
MetaSVM	Uncertain	0.21	D
MutationAssessor	Pathogenic	3.5	M
PhyloP100		0.15
PrimateAI	Pathogenic	0.88	D
PROVEAN	Pathogenic	-5.7	D
REVEL	Pathogenic	0.71
Sift	Uncertain	0.014	D
Sift4G	Pathogenic	0.0	D
Varity_R		0.92
gMVP		0.72
Mutation Taster		=43/56	disease causing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr12-122691269;