10-246791-C-T

Variant names:

• chr10-246791-C-T
• rs672601340
• NM_001370100.5:c.976C>T

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_001370100.5(ZMYND11):​c.976C>T​(p.Gln326*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. Q326Q) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZMYND11 NM_001370100.5 stop_gained
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 7.82
• Publications: 1 publications found

Genes affected

ZMYND11 (HGNC:16966): (zinc finger MYND-type containing 11) The protein encoded by this gene was first identified by its ability to bind the adenovirus E1A protein. The protein localizes to the nucleus. It functions as a transcriptional repressor, and expression of E1A inhibits this repression. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ZMYND11 Gene-Disease associations (from GenCC):

• syndromic complex neurodevelopmental disorder

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• intellectual disability, autosomal dominant 30

  Inheritance: AD Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• autosomal dominant non-syndromic intellectual disability

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

LOC107984190 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 11 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 10-246791-C-T is Pathogenic according to our data. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-246791-C-T is described in CliVar as Pathogenic. Clinvar id is 157552.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZMYND11	NM_001370100.5	c.976C>T	p.Gln326*	stop_gained	Exon 11 of 15	ENST00000381604.9	NP_001357029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZMYND11	ENST00000381604.9	c.976C>T	p.Gln326*	stop_gained	Exon 11 of 15	5	NM_001370100.5	ENSP00000371017.6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Intellectual disability, autosomal dominant 30 Pathogenic:1

Oct 01, 2014

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.66
CADD	Pathogenic	39
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.91
FATHMM_MKL	Pathogenic	0.99	D
PhyloP100		7.8
Vest4		0.98
GERP RS		5.2
Mutation Taster		=0/200	disease causing (ClinVar)

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: rs672601340; hg19: chr10-292731;