GeneBe

rs768508482

Variant names:

Variant summary

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

The NM_006852.6(TLK2):​c.-19_-8delGGCGGCGGCGGC variant causes a splice region change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TLK2
NM_006852.6 splice_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.87

Publications

0 publications found
Variant links:
Genes affected
TLK2 (HGNC:11842): (tousled like kinase 2) This gene encodes a nuclear serine/threonine kinase that was first identified in Arabidopsis. The encoded protein is thought to function in the regulation of chromatin assembly in the S phase of the cell cycle by regulating the levels of a histone H3/H4 chaperone. This protein is associated with double-strand break repair of DNA damage caused by radiation. Pseudogenes of this gene are present on chromosomes 10 and 17. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
TLK2 Gene-Disease associations (from GenCC):
  • complex neurodevelopmental disorder
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • intellectual disability, autosomal dominant 57
    Inheritance: AD, SD Classification: DEFINITIVE, STRONG Submitted by: Illumina, Ambry Genetics, PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006852.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TLK2
NM_006852.6
MANE Select
c.-19_-8delGGCGGCGGCGGC
splice_region
Exon 1 of 22NP_006843.2
TLK2
NM_006852.6
MANE Select
c.-19_-8delGGCGGCGGCGGC
5_prime_UTR
Exon 1 of 22NP_006843.2
TLK2
NM_001284333.3
c.-16_-5delGGCGGCGGCGGC
splice_region
Exon 1 of 23NP_001271262.1Q86UE8-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TLK2
ENST00000346027.10
TSL:1 MANE Select
c.-19_-8delGGCGGCGGCGGC
splice_region
Exon 1 of 22ENSP00000275780.7Q86UE8-2
TLK2
ENST00000326270.13
TSL:1
c.-16_-5delGGCGGCGGCGGC
splice_region
Exon 1 of 23ENSP00000316512.9Q86UE8-1
TLK2
ENST00000343388.11
TSL:1
c.-19_-8delGGCGGCGGCGGC
splice_region
Exon 1 of 21ENSP00000340800.7Q86UE8-3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
15942
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
11904
African (AFR)
AF:
0.00
AC:
0
AN:
182
American (AMR)
AF:
0.00
AC:
0
AN:
172
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
108
East Asian (EAS)
AF:
0.00
AC:
0
AN:
544
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1288
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
154
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
56
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
12840
Other (OTH)
AF:
0.00
AC:
0
AN:
598
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs768508482; hg19: chr17-60556629; API