rs869312859

Positions:

• chr17-7204200-T-TA

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_001321075.3(DLG4):​c.148dupT​(p.Tyr50fs) variant causes a frameshift, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DLG4 NM_001321075.3 frameshift, splice_region
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 8.17

Genes affected

DLG4 (HGNC:2903): (discs large MAGUK scaffold protein 4) This gene encodes a member of the membrane-associated guanylate kinase (MAGUK) family. It heteromultimerizes with another MAGUK protein, DLG2, and is recruited into NMDA receptor and potassium channel clusters. These two MAGUK proteins may interact at postsynaptic sites to form a multimeric scaffold for the clustering of receptors, ion channels, and associated signaling proteins. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

DLG4 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 18 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 17-7204200-T-TA is Pathogenic according to our data. Variant chr17-7204200-T-TA is described in ClinVar as [Likely_pathogenic]. Clinvar id is 224807.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLG4	NM_001321075.3	c.148dupT	p.Tyr50fs	frameshift_variant, splice_region_variant	3/20	ENST00000399506.9	NP_001308004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLG4	ENST00000399506.9	c.148dupT	p.Tyr50fs	frameshift_variant, splice_region_variant	3/20	2	NM_001321075.3	ENSP00000382425.2
DLG4	ENST00000648172.8	c.277dupT	p.Tyr93fs	frameshift_variant, splice_region_variant	5/22			ENSP00000497806.3
DLG4	ENST00000648896.1	c.247dupT	p.Tyr83fs	frameshift_variant, splice_region_variant	3/20			ENSP00000497546.1
DLG4	ENST00000649520.1	c.-33dupT		splice_region_variant	2/19			ENSP00000497647.1
DLG4	ENST00000648263.1	c.-33dupT		splice_region_variant	1/14			ENSP00000498035.1
DLG4	ENST00000647975.1	c.82dupT	p.Tyr28fs	frameshift_variant, splice_region_variant	2/7			ENSP00000497912.1
DLG4	ENST00000451807.7	c.64dupT	p.Tyr22fs	frameshift_variant, splice_region_variant	2/8	5		ENSP00000407918.3
DLG4	ENST00000648658.1	c.160dupT	p.Tyr54fs	frameshift_variant, splice_region_variant	3/6			ENSP00000496903.1
DLG4	ENST00000648760.1	c.-33dupT		splice_region_variant	2/4			ENSP00000497462.1
DLG4	ENST00000650301.1	c.76dupT	p.Tyr26fs	frameshift_variant, splice_region_variant	2/4			ENSP00000497662.1
DLG4	ENST00000649520.1	c.-33dupT		5_prime_UTR_variant	2/19			ENSP00000497647.1
DLG4	ENST00000648263.1	c.-33dupT		5_prime_UTR_variant	1/14			ENSP00000498035.1
DLG4	ENST00000648760.1	c.-33dupT		5_prime_UTR_variant	2/4			ENSP00000497462.1
DLG4	ENST00000491753.2	n.277dupT		splice_region_variant, non_coding_transcript_exon_variant	5/21	2		ENSP00000467897.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Intellectual developmental disorder 62 Pathogenic:3

Pathogenic, no assertion criteria provided	literature only	OMIM	Dec 11, 2020	- -
Pathogenic, criteria provided, single submitter	research	Tumer Group, Copenhagen University Hospital, Rigshospitalet	Feb 28, 2023	- -
Pathogenic, criteria provided, single submitter	research	Institute of Human Genetics, University of Leipzig Medical Center	Dec 21, 2021	- -

Cerebral visual impairment and intellectual disability Pathogenic:1

Likely pathogenic, criteria provided, single submitter

research

Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine

Sep 09, 2015

This study shows that diverse genetic causes underlie CVI. -

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

LitVar

Other links and lift over

dbSNP: rs869312859; hg19: chr17-7107519;