GeneBe

rs33970984

Variant names:

Variant summary

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

The NM_015690.5(STK36):​c.434+58_434+68delTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000697 in 1,148,306 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000087 ( 0 hom., cov: 27)
Exomes 𝑓: 0.0000068 ( 0 hom. )

Consequence

STK36
NM_015690.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.12
Variant links:
Genes affected
STK36 (HGNC:17209): (serine/threonine kinase 36) This gene encodes a member of the serine/threonine kinase family of enzymes. This family member is similar to a Drosophila protein that plays a key role in the Hedgehog signaling pathway. This human protein is a positive regulator of the GLI zinc-finger transcription factors. Knockout studies of the homologous mouse gene suggest that defects in this human gene may lead to congenital hydrocephalus, possibly due to a functional defect in motile cilia. Because Hedgehog signaling is frequently activated in certain kinds of gastrointestinal cancers, it has been suggested that this gene is a target for the treatment of these cancers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]

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ACMG classification

Classification made for transcript

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
STK36NM_015690.5 linkc.434+58_434+68delTTTTTTTTTTT intron_variant Intron 5 of 26 ENST00000295709.8 NP_056505.2 Q9NRP7-1A0A140VJW1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STK36ENST00000295709.8 linkc.434+48_434+58delTTTTTTTTTTT intron_variant Intron 5 of 26 1 NM_015690.5 ENSP00000295709.3 Q9NRP7-1
STK36ENST00000392105.7 linkc.434+48_434+58delTTTTTTTTTTT intron_variant Intron 5 of 26 1 ENSP00000375954.3 Q9NRP7-2
STK36ENST00000440309.5 linkc.434+48_434+58delTTTTTTTTTTT intron_variant Intron 5 of 26 5 ENSP00000394095.1 Q9NRP7-1
STK36ENST00000424080.1 linkc.434+48_434+58delTTTTTTTTTTT intron_variant Intron 5 of 7 5 ENSP00000403527.1 C9JDA4

Frequencies

GnomAD3 genomes
AF:
0.00000871
AC:
1
AN:
114866
Hom.:
0
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000179
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000677
AC:
7
AN:
1033440
Hom.:
0
AF XY:
0.00000586
AC XY:
3
AN XY:
512336
show subpopulations
Gnomad4 AFR exome
AF:
0.0000925
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:
0.00000605
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000871
AC:
1
AN:
114866
Hom.:
0
Cov.:
27
AF XY:
0.0000183
AC XY:
1
AN XY:
54726
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000179
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs33970984; hg19: chr2-219540243; API