GeneBe

rs1717005

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_017886.4(ULK4):​c.1349-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. 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

ULK4
NM_017886.4 splice_region, intron

Scores

2
Splicing: ADA: 0.00001567
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.97

Publications

7 publications found
Variant links:
Genes affected
ULK4 (HGNC:15784): (unc-51 like kinase 4) This gene encodes a member of the unc-51-like serine/threonine kinase (STK) family. Members of this protein family play a role in neuronal growth and endocytosis. The encoded protein is likely involved in neurite branching, neurite elongation and neuronal migration. Genome-wide association studies (GWAS) indicate an association of variations in this gene with blood pressure and hypertension. Sequence variations in this gene may also be be associated with psychiatric disorders, including schizophrenia and bipolar disorder. Pseudogenes associated with this gene have been identified and are located on chromosome 15. [provided by RefSeq, Jul 2016]
ULK4 Gene-Disease associations (from GenCC):
  • prostate cancer
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ULK4NM_017886.4 linkc.1349-5C>T splice_region_variant, intron_variant Intron 14 of 36 ENST00000301831.9 NP_060356.2
ULK4NM_001322500.2 linkc.1349-5C>T splice_region_variant, intron_variant Intron 14 of 35 NP_001309429.1
ULK4NM_001322501.2 linkc.443-5C>T splice_region_variant, intron_variant Intron 13 of 35 NP_001309430.1
ULK4NR_136342.2 linkn.1415-5C>T splice_region_variant, intron_variant Intron 13 of 34

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ULK4ENST00000301831.9 linkc.1349-5C>T splice_region_variant, intron_variant Intron 14 of 36 2 NM_017886.4 ENSP00000301831.4
ULK4ENST00000420927.5 linkc.1349-5C>T splice_region_variant, intron_variant Intron 14 of 17 1 ENSP00000412187.1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1451914
Hom.:
0
Cov.:
29
AF XY:
0.00
AC XY:
0
AN XY:
722520
African (AFR)
AF:
0.00
AC:
0
AN:
32938
American (AMR)
AF:
0.00
AC:
0
AN:
43084
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25854
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39606
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85792
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51744
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5708
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1107186
Other (OTH)
AF:
0.00
AC:
0
AN:
60002
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.42
DANN
Benign
0.95
PhyloP100
-2.0

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000016
dbscSNV1_RF
Benign
0.088
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

Other links and lift over

dbSNP: rs1717005; hg19: chr3-41938500; API