GeneBe

rs72173731

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001318374.2(PCDH9):​c.*10377_*10406dupATATATATATATATATATATATATATATAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00027 ( 7 hom., cov: 0)

Consequence

PCDH9
NM_001318374.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.114
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 made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 24 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PCDH9NM_203487.3 linkc.3036+10440_3036+10469dupATATATATATATATATATATATATATATAT intron_variant Intron 2 of 4 ENST00000377865.7 NP_982354.1 Q9HC56-1X5D7N0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PCDH9ENST00000377861 linkc.*10377_*10406dupATATATATATATATATATATATATATATAT 3_prime_UTR_variant Exon 2 of 2 1 ENSP00000367092.3 Q5VT82
PCDH9ENST00000377865.7 linkc.3036+10440_3036+10469dupATATATATATATATATATATATATATATAT intron_variant Intron 2 of 4 1 NM_203487.3 ENSP00000367096.2 Q9HC56-1
PCDH9ENST00000544246.5 linkc.3036+10440_3036+10469dupATATATATATATATATATATATATATATAT intron_variant Intron 2 of 3 1 ENSP00000442186.2 Q9HC56-2
PCDH9ENST00000456367.5 linkc.3036+10440_3036+10469dupATATATATATATATATATATATATATATAT intron_variant Intron 2 of 4 1 ENSP00000401699.2 B7ZM79

Frequencies

GnomAD3 genomes
AF:
0.000269
AC:
24
AN:
89240
Hom.:
7
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:
0.000324
Gnomad SAS
AF:
0.000322
Gnomad FIN
AF:
0.000360
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000449
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
0
GnomAD4 genome
AF:
0.000269
AC:
24
AN:
89282
Hom.:
7
Cov.:
0
AF XY:
0.000280
AC XY:
12
AN XY:
42904
show subpopulations
Gnomad4 AFR
AF:
0.0000444
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000325
Gnomad4 SAS
AF:
0.000322
Gnomad4 FIN
AF:
0.000360
Gnomad4 NFE
AF:
0.000449
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs66460017; hg19: chr13-67789067; API