13-19993408-TGTAA-T

Variant names:

• chr13-19993408-TGTAA-T
• NM_197968.4:c.339_342delAAGT

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_197968.4(ZMYM2):​c.339_342delAAGT​(p.Ser114ArgfsTer51) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZMYM2 NM_197968.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 4.24

Genes affected

ZMYM2 (HGNC:12989): (zinc finger MYM-type containing 2) The protein encoded by this gene is a zinc finger protein that may act as a transcription factor. The encoded protein may be part of a BHC histone deacetylase complex. Translocation of this gene with the fibroblast growth factor receptor-1 gene (FGFR1) results in a fusion gene, which may be a cause of stem cell leukemia lymphoma syndrome (SCLL). Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Pathogenic. Variant got 12 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
• PP5: Variant 13-19993408-TGTAA-T is Pathogenic according to our data. Variant chr13-19993408-TGTAA-T is described in ClinVar as [Pathogenic]. Clinvar id is 3767150.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZMYM2	NM_197968.4	c.339_342delAAGT	p.Ser114ArgfsTer51	frameshift_variant	Exon 3 of 25	ENST00000610343.5	NP_932072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZMYM2	ENST00000610343.5	c.339_342delAAGT	p.Ser114ArgfsTer51	frameshift_variant	Exon 3 of 25	1	NM_197968.4	ENSP00000479904.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities Pathogenic:1

-

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

A novel frameshift deletion, c.339_342del in exon 3 of ZMYM2 was observed in heterozygous state in proband. Sanger validation and segregation analysis showed that this variant was present in heterozygous state in the proband and in wild-type state in his parents. This variant is absent in population database gnomAD (v4.1.0) and our in-house database of 3527 exomes.The variant may cause shift in the reading frame of the transcript which likely introduces a premature termination codon. This may either result in a formation of truncated protein product or cause the transcript to undergo nonsense-mediated mRNA decay. -

Computational scores

Source: dbNSFP v4.3

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr13-20567548;