NM_015690.5:c.434+66_434+68delTTT

Variant names:

• chr2-218675520-CTTT-C
• rs33970984
• NM_015690.5:c.434+66_434+68delTTT

Variant summary

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

The NM_015690.5(STK36):​c.434+66_434+68delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0179 in 1,120,178 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 0.000035 (0 hom., cov: 27)
  • Exomes 𝑓: 0.020 (0 hom.)
• Consequence: STK36 NM_015690.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• ciliary dyskinesia, primary, 46

  Inheritance: AR Classification: MODERATE, LIMITED Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015690.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK36	NM_015690.5	MANE Select	c.434+66_434+68delTTT		intron	N/A	NP_056505.2	Q9NRP7-1
	STK36	NM_001369423.1		c.434+66_434+68delTTT		intron	N/A	NP_001356352.1	Q9NRP7-1
	STK36	NM_001243313.2		c.434+66_434+68delTTT		intron	N/A	NP_001230242.1	Q9NRP7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK36	ENST00000295709.8	TSL:1 MANE Select	c.434+48_434+50delTTT		intron	N/A	ENSP00000295709.3	Q9NRP7-1
	STK36	ENST00000392105.7	TSL:1	c.434+48_434+50delTTT		intron	N/A	ENSP00000375954.3	Q9NRP7-2
	STK36	ENST00000440309.5	TSL:5	c.434+48_434+50delTTT		intron	N/A	ENSP00000394095.1	Q9NRP7-1

Frequencies

GnomAD3 genomes AF: 0.0000348 AC: 4 AN: 114860 Hom.: 0 Cov.: 27

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000878

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: 0.0000358

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0352 AC: 2086 AN: 59338 AF XY: 0.0358

Gnomad AFR exome AF: 0.0448

Gnomad AMR exome AF: 0.0303

Gnomad ASJ exome AF: 0.0268

Gnomad EAS exome AF: 0.0424

Gnomad FIN exome AF: 0.0408

Gnomad NFE exome AF: 0.0336

Gnomad OTH exome AF: 0.0298

GnomAD4 exome AF: 0.0200 AC: 20057 AN: 1005316 Hom.: 0 AF XY: 0.0200 AC XY: 9971 AN XY: 498026

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0343 AC: 720 AN: 21010

American (AMR) AF: 0.0210 AC: 408 AN: 19402

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 387 AN: 14462

East Asian (EAS) AF: 0.0339 AC: 823 AN: 24272

South Asian (SAS) AF: 0.0209 AC: 1151 AN: 55052

European-Finnish (FIN) AF: 0.0262 AC: 615 AN: 23470

Middle Eastern (MID) AF: 0.0239 AC: 63 AN: 2634

European-Non Finnish (NFE) AF: 0.0186 AC: 14986 AN: 805178

Other (OTH) AF: 0.0227 AC: 904 AN: 39836

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0000348 AC: 4 AN: 114862 Hom.: 0 Cov.: 27 AF XY: 0.0000548 AC XY: 3 AN XY: 54748

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 28696

American (AMR) AF: 0.0000877 AC: 1 AN: 11408

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2944

East Asian (EAS) AF: 0.00 AC: 0 AN: 3954

South Asian (SAS) AF: 0.00 AC: 0 AN: 3570

European-Finnish (FIN) AF: 0.000173 AC: 1 AN: 5794

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 232

European-Non Finnish (NFE) AF: 0.0000358 AC: 2 AN: 55920

Other (OTH) AF: 0.00 AC: 0 AN: 1596

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.0634128), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00104 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs33970984; hg19: chr2-219540243;