20-54568983-C-CAAAA

Variant names:

• chr20-54568983-C-CAAAA
• rs10542523
• NM_018431.5:c.174+13962_174+13965dupAAAA

Variant summary

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

The NM_018431.5(DOK5):​c.174+13962_174+13965dupAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: DOK5 NM_018431.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 4 publications found

Genes affected

DOK5 (HGNC:16173): (docking protein 5) The protein encoded by this gene is a member of the DOK family of membrane proteins, which are adapter proteins involved in signal transduction. The encoded protein interacts with phosphorylated receptor tyrosine kinases to mediate neurite outgrowth and activation of the MAP kinase pathway. Unlike other DOK family proteins, this protein does not interact with RASGAP. This protein is up-regulated in patients with systemic sclerosis and is associated with fibrosis induced by insulin-like growth factor binding protein 5. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jun 2014]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018431.5. 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
	DOK5	NM_018431.5	MANE Select	c.174+13962_174+13965dupAAAA		intron	N/A	NP_060901.2
	DOK5	NM_177959.3		c.-151+13962_-151+13965dupAAAA		intron	N/A	NP_808874.1	Q9P104-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DOK5	ENST00000262593.10	TSL:1 MANE Select	c.174+13943_174+13944insAAAA		intron	N/A	ENSP00000262593.5	Q9P104-1
	DOK5	ENST00000395939.5	TSL:1	c.-151+13943_-151+13944insAAAA		intron	N/A	ENSP00000379270.1	Q9P104-2
	DOK5	ENST00000939307.1		c.174+13943_174+13944insAAAA		intron	N/A	ENSP00000609366.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 96234 Hom.: 0 Cov.: 0

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: 0.00

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 96234 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 44786

African (AFR) AF: 0.00 AC: 0 AN: 26900

American (AMR) AF: 0.00 AC: 0 AN: 8944

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2486

East Asian (EAS) AF: 0.00 AC: 0 AN: 3336

South Asian (SAS) AF: 0.00 AC: 0 AN: 2530

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3448

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 196

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 46542

Other (OTH) AF: 0.00 AC: 0 AN: 1262

Alfa AF: 0.00 Hom.: 1186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10542523; hg19: chr20-53185522;