13-52087453-C-A

Variant names:

• chr13-52087453-C-A
• rs770857581
• NM_001365552.1:c.1277G>T

Variant summary

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

The NM_001365552.1(NEK5):​c.1277G>T​(p.Gly426Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000146 in 1,366,580 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: NEK5 NM_001365552.1 missense, splice_region
• Scores: Splicing: ADA: 0.9743
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.81

Genes affected

NEK5 (HGNC:7748): (NIMA related kinase 5) Predicted to enable ATP binding activity; metal ion binding activity; and protein kinase activity. Predicted to be involved in protein phosphorylation. Predicted to act upstream of or within positive regulation of cysteine-type endopeptidase activity and positive regulation of striated muscle cell differentiation. [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
NEK5	NM_001365552.1	c.1277G>T	p.Gly426Val	missense_variant, splice_region_variant	Exon 15 of 24	ENST00000684899.1	NP_001352481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEK5	ENST00000684899.1	c.1277G>T	p.Gly426Val	missense_variant, splice_region_variant	Exon 15 of 24		NM_001365552.1	ENSP00000509632.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000146 AC: 2 AN: 1366580 Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0 AN XY: 684070

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000194

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Sep 01, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1277G>T (p.G426V) alteration is located in exon 15 (coding exon 13) of the NEK5 gene. This alteration results from a G to T substitution at nucleotide position 1277, causing the glycine (G) at amino acid position 426 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Uncertain	0.13	D
BayesDel_noAF	Uncertain	-0.050
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.027	.;T;T
Eigen	Uncertain	0.66
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.88	D;.;D
M_CAP	Benign	0.055	D
MetaRNN	Uncertain	0.54	D;D;D
MetaSVM	Uncertain	0.23	D
MutationAssessor	Uncertain	2.5	.;M;M
PrimateAI	Uncertain	0.52	T
PROVEAN	Pathogenic	-6.4	.;D;.
REVEL	Uncertain	0.38
Sift	Uncertain	0.0030	.;D;.
Sift4G	Uncertain	0.011	.;D;D
Polyphen		1.0	.;D;D
Vest4		0.65
MutPred		0.26		Loss of helix (P = 0.079);Loss of helix (P = 0.079);Loss of helix (P = 0.079);
MVP		0.93
MPC		0.41
ClinPred		1.0	D
GERP RS		5.5
Varity_R		0.81
gMVP		0.26

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.97
dbscSNV1_RF	Pathogenic	0.83
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: rs770857581; hg19: chr13-52661589;