rs765314519

Variant names:

• chr14-50114373-T-A
• rs765314519
• NM_024558.3:c.482A>T

Your query was ambiguous. Multiple possible variants found:

• chr14-50114373-T-A
• chr14-50114373-T-C

Variant summary

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

The NM_024558.3(VCPKMT):​c.482A>T​(p.Asp161Val) 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)
• Consequence: VCPKMT NM_024558.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.13

Genes affected

VCPKMT (HGNC:20352): (valosin containing protein lysine methyltransferase) Enables ATPase binding activity and protein-lysine N-methyltransferase activity. Involved in negative regulation of ATPase activity and peptidyl-lysine trimethylation. Located in cytosol. Part of protein-containing complex. [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
VCPKMT	NM_024558.3	c.482A>T	p.Asp161Val	missense_variant	Exon 4 of 6	ENST00000395860.7	NP_078834.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VCPKMT	ENST00000395860.7	c.482A>T	p.Asp161Val	missense_variant	Exon 4 of 6	1	NM_024558.3	ENSP00000379201.2

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	Benign	0.19
BayesDel_addAF	Uncertain	0.056	T
BayesDel_noAF	Benign	-0.16
CADD	Uncertain	24
DANN	Uncertain	0.97
DEOGEN2	Benign	0.022	T;.
Eigen	Benign	-0.012
Eigen_PC	Benign	0.13
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Uncertain	0.91	D;D
M_CAP	Benign	0.014	T
MetaRNN	Uncertain	0.66	D;D
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.5	M;M
PrimateAI	Uncertain	0.50	T
PROVEAN	Uncertain	-3.2	D;D
REVEL	Benign	0.19
Sift	Benign	0.29	T;T
Sift4G	Benign	0.32	T;T
Polyphen		0.036	B;.
Vest4		0.73
MutPred		0.59		Gain of catalytic residue at G164 (P = 0.0014);Gain of catalytic residue at G164 (P = 0.0014);
MVP		0.54
MPC		0.0062
ClinPred		0.77	D
GERP RS		5.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.69
gMVP		0.63

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: rs765314519; hg19: chr14-50581091; COSMIC: COSV99365676; COSMIC: COSV99365676;