Variant 2-218675520-CTTTTTTTTTTT-CTTTTTTT details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015690.5(STK36):c.434+65_434+68delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00367 in 1,137,620 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: 0.0041 ( 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]

STK36 links:

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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
STK36	NM_015690.5 link	c.434+65_434+68delTTTT		intron_variant	Intron 5 of 26	ENST00000295709.8	NP_056505.2	Q9NRP7-1A0A140VJW1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
STK36	ENST00000295709.8 link	c.434+48_434+51delTTTT	intron_variant	Intron 5 of 26	1	NM_015690.5	ENSP00000295709.3	Q9NRP7-1
STK36	ENST00000392105.7 link	c.434+48_434+51delTTTT	intron_variant	Intron 5 of 26	1		ENSP00000375954.3	Q9NRP7-2
STK36	ENST00000440309.5 link	c.434+48_434+51delTTTT	intron_variant	Intron 5 of 26	5		ENSP00000394095.1	Q9NRP7-1
STK36	ENST00000424080.1 link	c.434+48_434+51delTTTT	intron_variant	Intron 5 of 7	5		ENSP00000403527.1	C9JDA4

Frequencies

GnomAD3 genomes

AF:

0.00000871

AC:

AN:

114860

Hom.:

Cov.:

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:

0.000173

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00635

AC:

377

AN:

59338

Hom.:

AF XY:

0.00675

AC XY:

211

AN XY:

31242

show subpopulations

Gnomad AFR exome

AF:

0.00649

Gnomad AMR exome

AF:

0.00539

Gnomad ASJ exome

AF:

0.00330

Gnomad EAS exome

AF:

0.00739

Gnomad SAS exome

AF:

0.00806

Gnomad FIN exome

AF:

0.00823

Gnomad NFE exome

AF:

0.00623

Gnomad OTH exome

AF:

0.00516

GnomAD4 exome

AF:

0.00409

AC:

4179

AN:

1022760

Hom.:

AF XY:

0.00408

AC XY:

2069

AN XY:

506930

show subpopulations

Gnomad4 AFR exome

AF:

0.00732

Gnomad4 AMR exome

AF:

0.00461

Gnomad4 ASJ exome

AF:

0.00687

Gnomad4 EAS exome

AF:

0.00839

Gnomad4 SAS exome

AF:

0.00395

Gnomad4 FIN exome

AF:

0.00617

Gnomad4 NFE exome

AF:

0.00371

Gnomad4 OTH exome

AF:

0.00498

GnomAD4 genome

AF:

0.00000871

AC:

AN:

114860

Hom.:

Cov.:

AF XY:

0.0000183

AC XY:

AN XY:

54724

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:

0.000173

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over