NM_018921.3:c.1077C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_018921.3(PCDHGA9):​c.1077C>T​(p.Asp359Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 1,612,620 control chromosomes in the GnomAD database, including 175,243 homozygotes. 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: 𝑓 0.54 ( 24184 hom., cov: 31)
Exomes 𝑓: 0.45 ( 151059 hom. )

Consequence

PCDHGA9
NM_018921.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

25 publications found
Variant links:
Genes affected
PCDHGA9 (HGNC:8707): (protocadherin gamma subfamily A, 9) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGA4 (HGNC:8702): (protocadherin gamma subfamily A, 4) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGA2 (HGNC:8700): (protocadherin gamma subfamily A, 2) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGA3 (HGNC:8701): (protocadherin gamma subfamily A, 3) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGA6 (HGNC:8704): (protocadherin gamma subfamily A, 6) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGA7 (HGNC:8705): (protocadherin gamma subfamily A, 7) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGA8 (HGNC:8706): (protocadherin gamma subfamily A, 8) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGA1 (HGNC:8696): (protocadherin gamma subfamily A, 1) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGA5 (HGNC:8703): (protocadherin gamma subfamily A, 5) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGB2 (HGNC:8709): (protocadherin gamma subfamily B, 2) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGB3 (HGNC:8710): (protocadherin gamma subfamily B, 3) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGB1 (HGNC:8708): (protocadherin gamma subfamily B, 1) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGB4 (HGNC:8711): (protocadherin gamma subfamily B, 4) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. This particular family member is expressed in fibroblasts and is thought to play a role in wound healing in response to injury. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PCDHGB5 (HGNC:8712): (protocadherin gamma subfamily B, 5) This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP7
Synonymous conserved (PhyloP=-1.03 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PCDHGA9NM_018921.3 linkc.1077C>T p.Asp359Asp synonymous_variant Exon 1 of 4 ENST00000573521.2 NP_061744.1
PCDHGA4NM_018917.4 linkc.2514+46408C>T intron_variant Intron 1 of 3 ENST00000571252.3 NP_061740.2
PCDHGA2NM_018915.4 linkc.2424+62634C>T intron_variant Intron 1 of 3 ENST00000394576.3 NP_061738.1
PCDHGA3NM_018916.4 linkc.2424+57572C>T intron_variant Intron 1 of 3 ENST00000253812.8 NP_061739.2
PCDHGA6NM_018919.3 linkc.2424+27522C>T intron_variant Intron 1 of 3 ENST00000517434.3 NP_061742.1
PCDHGA7NM_018920.4 linkc.2424+18706C>T intron_variant Intron 1 of 3 ENST00000518325.2 NP_061743.1
PCDHGA8NM_032088.2 linkc.2424+8792C>T intron_variant Intron 1 of 3 ENST00000398604.3 NP_114477.1
PCDHGA1NM_018912.3 linkc.2421+70924C>T intron_variant Intron 1 of 3 ENST00000517417.3 NP_061735.1
PCDHGA5NM_018918.3 linkc.2421+37278C>T intron_variant Intron 1 of 3 ENST00000518069.2 NP_061741.1
PCDHGB2NM_018923.3 linkc.2421+41473C>T intron_variant Intron 1 of 3 ENST00000522605.2 NP_061746.1
PCDHGB3NM_018924.5 linkc.2415+31220C>T intron_variant Intron 1 of 3 ENST00000576222.2 NP_061747.2
PCDHGB1NM_018922.3 linkc.2409+51360C>T intron_variant Intron 1 of 3 ENST00000523390.2 NP_061745.1
PCDHGB4NM_003736.4 linkc.2397+13748C>T intron_variant Intron 1 of 3 ENST00000519479.2 NP_003727.1
PCDHGB5NM_018925.3 linkc.2397+3505C>T intron_variant Intron 1 of 3 ENST00000617380.2 NP_061748.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PCDHGA9ENST00000573521.2 linkc.1077C>T p.Asp359Asp synonymous_variant Exon 1 of 4 1 NM_018921.3 ENSP00000460274.1
PCDHGA4ENST00000571252.3 linkc.2514+46408C>T intron_variant Intron 1 of 3 1 NM_018917.4 ENSP00000458570.2
PCDHGA3ENST00000253812.8 linkc.2424+57572C>T intron_variant Intron 1 of 3 1 NM_018916.4 ENSP00000253812.7
PCDHGA2ENST00000394576.3 linkc.2424+62634C>T intron_variant Intron 1 of 3 1 NM_018915.4 ENSP00000378077.2
PCDHGA8ENST00000398604.3 linkc.2424+8792C>T intron_variant Intron 1 of 3 1 NM_032088.2 ENSP00000381605.2
PCDHGA6ENST00000517434.3 linkc.2424+27522C>T intron_variant Intron 1 of 3 1 NM_018919.3 ENSP00000429601.2
PCDHGA7ENST00000518325.2 linkc.2424+18706C>T intron_variant Intron 1 of 3 1 NM_018920.4 ENSP00000430024.1
PCDHGA1ENST00000517417.3 linkc.2421+70924C>T intron_variant Intron 1 of 3 1 NM_018912.3 ENSP00000431083.1
PCDHGA5ENST00000518069.2 linkc.2421+37278C>T intron_variant Intron 1 of 3 1 NM_018918.3 ENSP00000429834.1
PCDHGB2ENST00000522605.2 linkc.2421+41473C>T intron_variant Intron 1 of 3 1 NM_018923.3 ENSP00000429018.1
PCDHGB3ENST00000576222.2 linkc.2415+31220C>T intron_variant Intron 1 of 3 1 NM_018924.5 ENSP00000461862.1
PCDHGB1ENST00000523390.2 linkc.2409+51360C>T intron_variant Intron 1 of 3 1 NM_018922.3 ENSP00000429273.1
PCDHGB4ENST00000519479.2 linkc.2397+13748C>T intron_variant Intron 1 of 3 1 NM_003736.4 ENSP00000428288.1
PCDHGB5ENST00000617380.2 linkc.2397+3505C>T intron_variant Intron 1 of 3 1 NM_018925.3 ENSP00000478258.1

Frequencies

GnomAD3 genomes
AF:
0.540
AC:
81927
AN:
151796
Hom.:
24124
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.794
Gnomad AMI
AF:
0.357
Gnomad AMR
AF:
0.576
Gnomad ASJ
AF:
0.361
Gnomad EAS
AF:
0.339
Gnomad SAS
AF:
0.429
Gnomad FIN
AF:
0.424
Gnomad MID
AF:
0.420
Gnomad NFE
AF:
0.431
Gnomad OTH
AF:
0.501
GnomAD2 exomes
AF:
0.475
AC:
118184
AN:
249000
AF XY:
0.462
show subpopulations
Gnomad AFR exome
AF:
0.804
Gnomad AMR exome
AF:
0.661
Gnomad ASJ exome
AF:
0.360
Gnomad EAS exome
AF:
0.322
Gnomad FIN exome
AF:
0.421
Gnomad NFE exome
AF:
0.430
Gnomad OTH exome
AF:
0.456
GnomAD4 exome
AF:
0.448
AC:
654155
AN:
1460704
Hom.:
151059
Cov.:
39
AF XY:
0.445
AC XY:
323189
AN XY:
726678
show subpopulations
African (AFR)
AF:
0.806
AC:
26964
AN:
33472
American (AMR)
AF:
0.651
AC:
29092
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
0.363
AC:
9490
AN:
26122
East Asian (EAS)
AF:
0.354
AC:
14070
AN:
39696
South Asian (SAS)
AF:
0.431
AC:
37126
AN:
86172
European-Finnish (FIN)
AF:
0.419
AC:
22375
AN:
53378
Middle Eastern (MID)
AF:
0.438
AC:
2528
AN:
5766
European-Non Finnish (NFE)
AF:
0.436
AC:
484825
AN:
1111040
Other (OTH)
AF:
0.459
AC:
27685
AN:
60338
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.471
Heterozygous variant carriers
0
19135
38271
57406
76542
95677
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
14944
29888
44832
59776
74720
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.540
AC:
82048
AN:
151916
Hom.:
24184
Cov.:
31
AF XY:
0.538
AC XY:
39918
AN XY:
74240
show subpopulations
African (AFR)
AF:
0.794
AC:
32909
AN:
41448
American (AMR)
AF:
0.577
AC:
8815
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.361
AC:
1252
AN:
3472
East Asian (EAS)
AF:
0.339
AC:
1740
AN:
5126
South Asian (SAS)
AF:
0.428
AC:
2053
AN:
4800
European-Finnish (FIN)
AF:
0.424
AC:
4456
AN:
10516
Middle Eastern (MID)
AF:
0.415
AC:
122
AN:
294
European-Non Finnish (NFE)
AF:
0.431
AC:
29320
AN:
67958
Other (OTH)
AF:
0.501
AC:
1055
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1764
3528
5291
7055
8819
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
688
1376
2064
2752
3440
<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:
0.459
Hom.:
21445
Bravo
AF:
0.565
Asia WGS
AF:
0.437
AC:
1522
AN:
3478
EpiCase
AF:
0.428
EpiControl
AF:
0.421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
10
DANN
Benign
0.86
PhyloP100
-1.0
Mutation Taster
=99/1
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs1363448; hg19: chr5-140783596; COSMIC: COSV53936367; COSMIC: COSV53936367; API