DLGAP2 p.Ser136*

Variant names:

• chr8-910549-AGC-TAG
• NM_001346810.2:c.73+2583_73+2585delAGCinsTAG

Your query was ambiguous. Multiple possible variants found:

• chr8-910549-AGC-TAG
• chr8-910549-AGC-TAA
• chr8-1549100-CC-AG
• chr8-1549100-CC-AA
• chr8-910549-AGC-TGA
• chr8-1548860-C-A
• chr8-1549100-CC-GA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001346810.2(DLGAP2):​c.73+2583_73+2585delAGCinsTAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DLGAP2 NM_001346810.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 0 publications found

Genes affected

DLGAP2 (HGNC:2906): (DLG associated protein 2) The product of this gene is a membrane-associated protein that may play a role in synapse organization and signalling in neuronal cells. This gene is biallelically expressed in the brain, however, only the paternal allele is expressed in the testis (PMID:18055845). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2014]

DLGAP2 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001346810.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP2	NM_001346810.2	MANE Select	c.73+2583_73+2585delAGCinsTAG		intron	N/A	NP_001333739.1	A0A1B0GTN4
	DLGAP2	NR_073397.2		n.355+2583_355+2585delAGCinsTAG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP2	ENST00000637795.2	TSL:5 MANE Select	c.73+2583_73+2585delAGCinsTAG		intron	N/A	ENSP00000489774.1	A0A1B0GTN4
	DLGAP2	ENST00000522092.5	TSL:1	n.332+2583_332+2585delAGCinsTAG		intron	N/A
	DLGAP2	ENST00000524139.5	TSL:1	n.206+2583_206+2585delAGCinsTAG		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr8-860549;