chr13-35850561-C-A

Variant names:

• chr13-35850561-C-A
• rs10507433
• ENST00000460982.1:c.*159G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000460982.1(DCLK1):​c.*159G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000018 in 1,109,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000018 (0 hom.)
• Consequence: DCLK1 ENST00000460982.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 7 publications found

Genes affected

DCLK1 (HGNC:2700): (doublecortin like kinase 1) This gene encodes a member of the protein kinase superfamily and the doublecortin family. The protein encoded by this gene contains two N-terminal doublecortin domains, which bind microtubules and regulate microtubule polymerization, a C-terminal serine/threonine protein kinase domain, which shows substantial homology to Ca2+/calmodulin-dependent protein kinase, and a serine/proline-rich domain in between the doublecortin and the protein kinase domains, which mediates multiple protein-protein interactions. The microtubule-polymerizing activity of the encoded protein is independent of its protein kinase activity. The encoded protein is involved in several different cellular processes, including neuronal migration, retrograde transport, neuronal apoptosis and neurogenesis. This gene is up-regulated by brain-derived neurotrophic factor and associated with memory and general cognitive abilities. Multiple transcript variants generated by two alternative promoter usage and alternative splicing have been reported, but the full-length nature and biological validity of some variants have not been defined. These variants encode different isoforms, which are differentially expressed and have different kinase activities.[provided by RefSeq, Sep 2010]

ACMG classification

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460982.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCLK1	NM_001330071.2	MANE Select	c.1035+3938G>T		intron	N/A	NP_001317000.1
	DCLK1	NM_001438021.1		c.*159G>T		3_prime_UTR	Exon 7 of 7	NP_001424950.1
	DCLK1	NM_001195430.2		c.*159G>T		3_prime_UTR	Exon 3 of 3	NP_001182359.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCLK1	ENST00000460982.1	TSL:1	c.*159G>T		3_prime_UTR	Exon 3 of 3	ENSP00000516676.1
	DCLK1	ENST00000360631.8	TSL:5 MANE Select	c.1035+3938G>T		intron	N/A	ENSP00000353846.3
	DCLK1	ENST00000255448.8	TSL:1	c.1035+3938G>T		intron	N/A	ENSP00000255448.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000180 AC: 2 AN: 1109974 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 527128

African (AFR) AF: 0.00 AC: 0 AN: 23098

American (AMR) AF: 0.00 AC: 0 AN: 8824

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14610

East Asian (EAS) AF: 0.00 AC: 0 AN: 26540

South Asian (SAS) AF: 0.00 AC: 0 AN: 25544

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34316

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3028

European-Non Finnish (NFE) AF: 0.00000108 AC: 1 AN: 929536

Other (OTH) AF: 0.0000225 AC: 1 AN: 44478

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 6212

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.46
PhyloP100		-0.29

Splicing

Name	Calibrated prediction	Score	Prediction
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

Other links and lift over

dbSNP: rs10507433; hg19: chr13-36424698;