chr11-63902215-CA-C

Variant names:

• chr11-63902215-CA-C
• rs1554985733
• NM_001039469.3:c.1120delA

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_001039469.3(MARK2):​c.1120delA​(p.Thr374ProfsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MARK2 NM_001039469.3 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter P:1 U:1
• Conservation: PhyloP100: 1.36
• Publications: 0 publications found

Genes affected

MARK2 (HGNC:3332): (microtubule affinity regulating kinase 2) This gene encodes a member of the Par-1 family of serine/threonine protein kinases. The protein is an important regulator of cell polarity in epithelial and neuronal cells, and also controls the stability of microtubules through phosphorylation and inactivation of several microtubule-associating proteins. The protein localizes to cell membranes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039469.3. 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
	MARK2	NM_001039469.3	MANE Select	c.1120delA	p.Thr374ProfsTer2	frameshift	Exon 12 of 19	NP_001034558.2
	MARK2	NM_017490.4		c.1021delA	p.Thr341ProfsTer2	frameshift	Exon 12 of 18	NP_059672.2
	MARK2	NM_004954.5		c.1120delA	p.Thr374ProfsTer2	frameshift	Exon 12 of 17	NP_004945.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARK2	ENST00000402010.8	TSL:1 MANE Select	c.1120delA	p.Thr374ProfsTer2	frameshift	Exon 12 of 19	ENSP00000385751.2
	MARK2	ENST00000513765.7	TSL:1	c.1120delA	p.Thr374ProfsTer2	frameshift	Exon 12 of 18	ENSP00000421075.3
	MARK2	ENST00000425897.3	TSL:1	c.1120delA	p.Thr374ProfsTer2	frameshift	Exon 12 of 17	ENSP00000415494.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:1 Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Autism spectrum disorder Pathogenic:1

Jul 03, 2024

Department of Medical Genetics, Capital Institute of Pediatrics

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

PVS1+PM2_Supporting+PS2

not provided Uncertain:1

Nov 22, 2017

Mayo Clinic Laboratories, Mayo Clinic

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1554985733; hg19: chr11-63669687;