GeneBe

rs66460017

Variant names:

Variant summary

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

The NM_001318374.2(PCDH9):​c.*10377_*10406delATATATATATATATATATATATATATATAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, 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: 𝑓 0.000011 ( 0 hom., cov: 0)

Consequence

PCDH9
NM_001318374.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.719

Publications

0 publications found
Variant links:
Genes affected
PCDH9 (HGNC:8661): (protocadherin 9) This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Nov 2012]

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ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318374.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PCDH9
NM_203487.3
MANE Select
c.3036+10440_3036+10469delATATATATATATATATATATATATATATAT
intron
N/ANP_982354.1X5D7N0
PCDH9
NM_001318374.2
c.*10377_*10406delATATATATATATATATATATATATATATAT
3_prime_UTR
Exon 2 of 2NP_001305303.1Q5VT82
PCDH9
NM_020403.5
c.3036+10440_3036+10469delATATATATATATATATATATATATATATAT
intron
N/ANP_065136.1Q9HC56-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PCDH9
ENST00000377861.4
TSL:1
c.*10377_*10406delATATATATATATATATATATATATATATAT
3_prime_UTR
Exon 2 of 2ENSP00000367092.3Q5VT82
PCDH9
ENST00000377865.7
TSL:1 MANE Select
c.3036+10440_3036+10469delATATATATATATATATATATATATATATAT
intron
N/AENSP00000367096.2Q9HC56-1
PCDH9
ENST00000544246.5
TSL:1
c.3036+10440_3036+10469delATATATATATATATATATATATATATATAT
intron
N/AENSP00000442186.2Q9HC56-2

Frequencies

GnomAD3 genomes
AF:
0.0000112
AC:
1
AN:
89248
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000445
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000112
AC:
1
AN:
89248
Hom.:
0
Cov.:
0
AF XY:
0.0000233
AC XY:
1
AN XY:
42852
show subpopulations
African (AFR)
AF:
0.0000445
AC:
1
AN:
22470
American (AMR)
AF:
0.00
AC:
0
AN:
8194
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2484
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3086
South Asian (SAS)
AF:
0.00
AC:
0
AN:
3102
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
5562
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
164
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
42338
Other (OTH)
AF:
0.00
AC:
0
AN:
1154
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.72

Splicing

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

Publications

Other links and lift over

dbSNP: rs66460017; hg19: chr13-67789067; API