rs1057520011

Variant names:

• chr6-80038006-G-A
• rs1057520011
• NM_003318.5:c.2089G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-80038006-G-A
• chr6-80038006-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP3

The NM_003318.5(TTK):​c.2089G>A​(p.Asp697Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: TTK NM_003318.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.96
• Publications: 0 publications found

Genes affected

TTK (HGNC:12401): (TTK protein kinase) This gene encodes a dual specificity protein kinase with the ability to phosphorylate tyrosine, serine and threonine. Associated with cell proliferation, this protein is essential for chromosome alignment at the centromere during mitosis and is required for centrosome duplication. It has been found to be a critical mitotic checkpoint protein for accurate segregation of chromosomes during mitosis. Tumorigenesis may occur when this protein fails to degrade and produces excess centrosomes resulting in aberrant mitotic spindles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2009]

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.754

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTK	NM_003318.5	c.2089G>A	p.Asp697Asn	missense_variant	Exon 18 of 22	ENST00000369798.7	NP_003309.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTK	ENST00000369798.7	c.2089G>A	p.Asp697Asn	missense_variant	Exon 18 of 22	1	NM_003318.5	ENSP00000358813.2
TTK	ENST00000230510.7	c.2086G>A	p.Asp696Asn	missense_variant	Exon 18 of 22	2		ENSP00000230510.3
TTK	ENST00000509894.5	c.2086G>A	p.Asp696Asn	missense_variant	Exon 18 of 22	5		ENSP00000422936.1
TTK	ENST00000504590.1	n.454G>A		non_coding_transcript_exon_variant	Exon 1 of 3	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1458494 Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1 AN XY: 725592

African (AFR) AF: 0.00 AC: 0 AN: 33352

American (AMR) AF: 0.00 AC: 0 AN: 44492

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26010

East Asian (EAS) AF: 0.00 AC: 0 AN: 39564

South Asian (SAS) AF: 0.00 AC: 0 AN: 85856

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53184

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5738

European-Non Finnish (NFE) AF: 9.01e-7 AC: 1 AN: 1110100

Other (OTH) AF: 0.00 AC: 0 AN: 60198

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Benign	-0.070	T
BayesDel_noAF	Benign	-0.34
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Benign	0.19	.;.;T
Eigen	Uncertain	0.48
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.88	.;D;D
M_CAP	Benign	0.052	D
MetaRNN	Pathogenic	0.75	D;D;D
MetaSVM	Benign	-0.46	T
MutationAssessor	Benign	0.12	.;.;N
PhyloP100		9.0
PrimateAI	Uncertain	0.77	T
PROVEAN	Uncertain	-3.3	D;D;D
REVEL	Uncertain	0.38
Sift	Benign	0.047	D;D;T
Sift4G	Uncertain	0.043	D;D;D
Polyphen		0.99	.;.;D
Vest4		0.71
MutPred		0.38		.;.;Loss of solvent accessibility (P = 0.0387);
MVP		0.69
MPC		0.26
ClinPred		0.97	D
GERP RS		4.0
Varity_R		0.51
gMVP		0.71
Mutation Taster		=45/55	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1057520011; hg19: chr6-80747723;