rs10542523

chr20-54568983-CAAAAAAA-Cchr20-54568983-CAAAAAAA-CAchr20-54568983-CAAAAAAA-CAAchr20-54568983-CAAAAAAA-CAAAchr20-54568983-CAAAAAAA-CAAAAchr20-54568983-CAAAAAAA-CAAAAAchr20-54568983-CAAAAAAA-CAAAAAAchr20-54568983-CAAAAAAA-CAAAAAAAAchr20-54568983-CAAAAAAA-CAAAAAAAAAchr20-54568983-CAAAAAAA-CAAAAAAAAAAchr20-54568983-CAAAAAAA-CAAAAAAAAAAAchr20-54568983-CAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAAchr20-54568983-CAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAchr20-54568983-CAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAATAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

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

The NM_018431.5(DOK5):c.174+13959_174+13965del 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: 1.42

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOK5	NM_018431.5	c.174+13959_174+13965del		intron_variant		ENST00000262593.10
DOK5	NM_177959.3	c.-151+13959_-151+13965del		intron_variant
DOK5	XM_011528904.2	c.-151+13959_-151+13965del		intron_variant
DOK5	XM_024451946.2	c.138+13959_138+13965del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOK5	ENST00000262593.10	c.174+13959_174+13965del		intron_variant		1	NM_018431.5	P1
DOK5	ENST00000395939.5	c.-151+13959_-151+13965del		intron_variant		1

Frequencies

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

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

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: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10542523; hg19: chr20-53185522;