GeneBe

rs379266

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001197293.3(DPYSL2):​c.355-3376C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

DPYSL2
NM_001197293.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.161

Publications

1 publications found
Variant links:
Genes affected
DPYSL2 (HGNC:3014): (dihydropyrimidinase like 2) This gene encodes a member of the collapsin response mediator protein family. Collapsin response mediator proteins form homo- and hetero-tetramers and facilitate neuron guidance, growth and polarity. The encoded protein promotes microtubule assembly and is required for Sema3A-mediated growth cone collapse, and also plays a role in synaptic signaling through interactions with calcium channels. This gene has been implicated in multiple neurological disorders, and hyperphosphorylation of the encoded protein may play a key role in the development of Alzheimer's disease. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]
DPYSL2 Gene-Disease associations (from GenCC):
  • schizophrenia
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001197293.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DPYSL2
NM_001197293.3
MANE Select
c.355-3376C>A
intron
N/ANP_001184222.1A0A1C7CYX9
DPYSL2
NM_001386.6
c.39+300C>A
intron
N/ANP_001377.1Q16555-1
DPYSL2
NM_001244604.2
c.-70+60C>A
intron
N/ANP_001231533.1Q16555-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DPYSL2
ENST00000521913.7
TSL:1 MANE Select
c.355-3376C>A
intron
N/AENSP00000427985.2A0A1C7CYX9
DPYSL2
ENST00000311151.9
TSL:1
c.39+300C>A
intron
N/AENSP00000309539.5Q16555-1
DPYSL2
ENST00000523027.1
TSL:2
c.-70+60C>A
intron
N/AENSP00000431117.1Q16555-2

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1134384
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
543726
African (AFR)
AF:
0.00
AC:
0
AN:
23982
American (AMR)
AF:
0.00
AC:
0
AN:
10834
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
14854
East Asian (EAS)
AF:
0.00
AC:
0
AN:
22110
South Asian (SAS)
AF:
0.00
AC:
0
AN:
47580
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
18426
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2978
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
948198
Other (OTH)
AF:
0.00
AC:
0
AN:
45422
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.00
Hom.:
5507

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
CADD
Benign
8.5
DANN
Benign
0.86
PhyloP100
0.16
PromoterAI
-0.0013
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs379266; hg19: chr8-26436109; API