dbSNP rs33970984: STK36:c.434+56_434+68delTTTTTTTTTTTTT (chr2-218675520-CTTTTTTTTTTTTT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_015690.5(STK36):c.434+56_434+68delTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000968 in 1,033,442 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 27)

Exomes 𝑓: 9.7e-7 ( 0 hom. )

Consequence

STK36
NM_015690.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.12

Publications

0 publications found

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 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

STK36 links:

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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_015690.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STK36	NM_015690.5	MANE Select	c.434+56_434+68delTTTTTTTTTTTTT	intron	N/A	NP_056505.2	Q9NRP7-1
STK36	NM_001369423.1		c.434+56_434+68delTTTTTTTTTTTTT	intron	N/A	NP_001356352.1	Q9NRP7-1
STK36	NM_001243313.2		c.434+56_434+68delTTTTTTTTTTTTT	intron	N/A	NP_001230242.1	Q9NRP7-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STK36	ENST00000295709.8	TSL:1 MANE Select	c.434+48_434+60delTTTTTTTTTTTTT	intron	N/A	ENSP00000295709.3	Q9NRP7-1
STK36	ENST00000392105.7	TSL:1	c.434+48_434+60delTTTTTTTTTTTTT	intron	N/A	ENSP00000375954.3	Q9NRP7-2
STK36	ENST00000440309.5	TSL:5	c.434+48_434+60delTTTTTTTTTTTTT	intron	N/A	ENSP00000394095.1	Q9NRP7-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

9.68e-7

AC:

AN:

1033442

Hom.:

AF XY:

0.00

AC XY:

AN XY:

512336

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

21618

American (AMR)

AF:

0.00

AC:

AN:

20256

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14854

East Asian (EAS)

AF:

0.00

AC:

AN:

25138

South Asian (SAS)

AF:

0.00

AC:

AN:

57458

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24144

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2704

European-Non Finnish (NFE)

AF:

0.00000121

AC:

AN:

826296

Other (OTH)

AF:

0.00

AC:

AN:

40974

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over