NM_001384711.1:c.454G>C

Variant names:

• chr12-103997484-C-G
• rs543467029
• NM_001384711.1:c.454G>C

Variant summary

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

The NM_001384711.1(GLT8D2):​c.454G>C​(p.Val152Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. V152I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GLT8D2 NM_001384711.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.96

Genes affected

GLT8D2 (HGNC:24890): (glycosyltransferase 8 domain containing 2) Predicted to enable glycosyltransferase activity. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

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
GLT8D2	NM_001384711.1	c.454G>C	p.Val152Leu	missense_variant	Exon 7 of 11	ENST00000360814.9	NP_001371640.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLT8D2	ENST00000360814.9	c.454G>C	p.Val152Leu	missense_variant	Exon 7 of 11	1	NM_001384711.1	ENSP00000354053.4
GLT8D2	ENST00000546436.5	c.454G>C	p.Val152Leu	missense_variant	Exon 6 of 10	5		ENSP00000449750.1
GLT8D2	ENST00000548660.5	c.454G>C	p.Val152Leu	missense_variant	Exon 7 of 11	2		ENSP00000447450.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.49
BayesDel_addAF	Uncertain	0.014	T
BayesDel_noAF	Benign	-0.22
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.29	T;T;T
Eigen	Uncertain	0.56
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.87	.;.;D
M_CAP	Benign	0.012	T
MetaRNN	Uncertain	0.57	D;D;D
MetaSVM	Benign	-0.99	T
MutationAssessor	Uncertain	2.4	M;M;M
PrimateAI	Uncertain	0.67	T
PROVEAN	Benign	-1.5	N;N;N
REVEL	Benign	0.16
Sift	Benign	0.18	T;T;T
Sift4G	Benign	0.26	T;T;T
Polyphen		0.96	D;D;D
Vest4		0.62
MutPred		0.58		Gain of catalytic residue at E150 (P = 0.0042);Gain of catalytic residue at E150 (P = 0.0042);Gain of catalytic residue at E150 (P = 0.0042);
MVP		0.36
MPC		0.38
ClinPred		0.91	D
GERP RS		5.4
Varity_R		0.27
gMVP		0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs543467029; hg19: chr12-104391262;