NM_145010.4:c.568G>T

Variant names:

• chr10-24990489-C-A
• rs367769430
• NM_145010.4:c.568G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_145010.4(ENKUR):​c.568G>T​(p.Asp190Tyr) 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. D190N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ENKUR NM_145010.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.12
• Publications: 4 publications found

Genes affected

ENKUR (HGNC:28388): (enkurin, TRPC channel interacting protein) This gene encodes a protein that interacts with calmodulin and several transient receptor potential canonical cation channel proteins. The encoded protein may function as an adaptor to localize signal transduction machinery to calcium channels. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

ENSG00000285859 (HGNC:):

THNSL1 (HGNC:26160): (threonine synthase like 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 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
ENKUR	NM_145010.4	c.568G>T	p.Asp190Tyr	missense_variant	Exon 4 of 6	ENST00000331161.9	NP_659447.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENKUR	ENST00000331161.9	c.568G>T	p.Asp190Tyr	missense_variant	Exon 4 of 6	1	NM_145010.4	ENSP00000331044.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Uncertain	0.010
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.094	T;.;T;T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.89	.;D;D;D
M_CAP	Benign	0.0050	T
MetaRNN	Uncertain	0.67	D;D;D;D
MetaSVM	Benign	-0.39	T
MutationAssessor	Uncertain	2.2	M;.;.;.
PhyloP100		5.1
PrimateAI	Uncertain	0.50	T
PROVEAN	Uncertain	-4.2	D;.;D;.
REVEL	Benign	0.24
Sift	Benign	0.047	D;.;D;.
Sift4G	Uncertain	0.050	T;T;T;.
Polyphen		0.92	P;.;D;.
Vest4		0.62
MutPred		0.27		Loss of disorder (P = 0.0474);.;Loss of disorder (P = 0.0474);.;
MVP		0.14
MPC		0.14
ClinPred		0.98	D
GERP RS		5.9
Varity_R		0.36
gMVP		0.56
Mutation Taster		=62/38	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: rs367769430; hg19: chr10-25279418;