GeneBe

6-32152121-T-G

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001363780.2(PRRT1):​c.-19A>C variant causes a 5 prime UTR 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: 28)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PRRT1
NM_001363780.2 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.887

Publications

42 publications found
Variant links:
Genes affected
PRRT1 (HGNC:13943): (proline rich transmembrane protein 1) Enables identical protein binding activity. Predicted to be involved in several processes, including long-term synaptic depression; protein localization to cell surface; and regulation of AMPA receptor activity. Predicted to act upstream of or within several processes, including learning or memory; long-term synaptic potentiation; and synapse organization. Predicted to be located in postsynaptic density membrane and synaptic vesicle membrane. Predicted to be active in glutamatergic synapse and membrane. Predicted to be integral component of postsynaptic membrane. [provided by Alliance of Genome Resources, Apr 2022]
PPT2 (HGNC:9326): (palmitoyl-protein thioesterase 2) This gene encodes a member of the palmitoyl-protein thioesterase family. The encoded glycosylated lysosomal protein has palmitoyl-CoA hydrolase activity in vitro, but does not hydrolyze palmitate from cysteine residues in proteins. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream EGFL8 (EGF-like-domain, multiple 8) gene. [provided by RefSeq, Feb 2011]

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ACMG classification

Classification was made for transcript

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

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363780.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRRT1
NM_001363780.2
c.-19A>C
5_prime_UTR
Exon 2 of 6NP_001350709.1Q99946-2
PRRT1
NM_030651.4
MANE Select
c.-294A>C
upstream_gene
N/ANP_085154.3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRRT1
ENST00000375150.6
TSL:1
c.-99A>C
5_prime_UTR
Exon 2 of 6ENSP00000364292.3A0A8Z5AAT7
ENSG00000285085
ENST00000428778.5
TSL:3
c.-99A>C
5_prime_UTR
Exon 3 of 5ENSP00000396077.2A2ABC7
PPT2
ENST00000897785.1
c.-9+1532T>G
intron
N/AENSP00000567844.1

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
540486
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
292390
African (AFR)
AF:
0.00
AC:
0
AN:
15382
American (AMR)
AF:
0.00
AC:
0
AN:
33932
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19474
East Asian (EAS)
AF:
0.00
AC:
0
AN:
29324
South Asian (SAS)
AF:
0.00
AC:
0
AN:
61754
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
44610
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3970
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
302708
Other (OTH)
AF:
0.00
AC:
0
AN:
29332
GnomAD4 genome
Cov.:
28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
CADD
Benign
14
DANN
Benign
0.79
PhyloP100
-0.89
PromoterAI
0.042
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs3131283; hg19: chr6-32119898; API