Incidental Mutation 'R5021:Pcdhga1'
| ID |
389210 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga1
|
| Ensembl Gene |
ENSMUSG00000103144 |
| Gene Name |
protocadherin gamma subfamily A, 1 |
| Synonyms |
|
| MMRRC Submission |
042612-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5021 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37794846-37974926 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 37796876 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Serine
at position 627
(R627S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141367
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000115661]
[ENSMUST00000194190]
[ENSMUST00000194544]
[ENSMUST00000194888]
|
| AlphaFold |
Q91XZ0 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000115661
|
| SMART Domains |
Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
20 |
131 |
5.3e-2 |
SMART |
|
CA
|
155 |
240 |
1.51e-19 |
SMART |
|
CA
|
264 |
348 |
7.6e-25 |
SMART |
|
CA
|
372 |
453 |
1.42e-24 |
SMART |
|
CA
|
477 |
563 |
1.42e-24 |
SMART |
|
CA
|
594 |
674 |
4.12e-12 |
SMART |
|
low complexity region
|
706 |
721 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_tail
|
796 |
930 |
3.9e-58 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000192137
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000193984
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000194190
AA Change: R627S
PolyPhen 2
Score 0.938 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000142062
Gene: ENSMUSG00000103144
AA Change: R627S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
28 |
N/A |
INTRINSIC |
|
CA
|
31 |
131 |
3.16e-2 |
SMART |
|
CA
|
155 |
240 |
5.39e-16 |
SMART |
|
CA
|
264 |
345 |
6.72e-26 |
SMART |
|
CA
|
369 |
450 |
1.32e-24 |
SMART |
|
CA
|
474 |
560 |
4.17e-22 |
SMART |
|
CA
|
591 |
669 |
4.48e-13 |
SMART |
|
transmembrane domain
|
692 |
714 |
N/A |
INTRINSIC |
|
low complexity region
|
912 |
931 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194328
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194544
|
| SMART Domains |
Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:CA
|
18 |
66 |
5e-20 |
BLAST |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000194888
AA Change: R627S
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000141367
Gene: ENSMUSG00000103144
AA Change: R627S
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
28 |
N/A |
INTRINSIC |
|
CA
|
31 |
131 |
1.6e-4 |
SMART |
|
CA
|
155 |
240 |
2.7e-18 |
SMART |
|
CA
|
264 |
345 |
3.3e-28 |
SMART |
|
CA
|
369 |
450 |
6.7e-27 |
SMART |
|
CA
|
474 |
560 |
2e-24 |
SMART |
|
CA
|
591 |
669 |
2.2e-15 |
SMART |
|
transmembrane domain
|
692 |
714 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.4638 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.6%
- 20x: 89.8%
|
| Validation Efficiency |
95% (39/41) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] 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]
PHENOTYPE: Mice homozygous for a null/reporter allele are viable and fertile. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 35 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ano5 |
A |
T |
7: 51,205,933 (GRCm39) |
T242S |
probably benign |
Het |
| B3gnt4 |
G |
C |
5: 123,649,010 (GRCm39) |
R125P |
probably damaging |
Het |
| Blvrb |
A |
C |
7: 27,147,543 (GRCm39) |
M1L |
probably benign |
Het |
| Cep112 |
T |
A |
11: 108,361,154 (GRCm39) |
H169Q |
possibly damaging |
Het |
| Clcn1 |
A |
T |
6: 42,287,922 (GRCm39) |
K718* |
probably null |
Het |
| Clhc1 |
A |
G |
11: 29,510,627 (GRCm39) |
N226S |
probably benign |
Het |
| Cpne1 |
T |
C |
2: 155,940,193 (GRCm39) |
|
probably benign |
Het |
| Cspg4 |
G |
A |
9: 56,805,014 (GRCm39) |
V1942I |
probably benign |
Het |
| Decr2 |
A |
T |
17: 26,301,980 (GRCm39) |
L250Q |
probably damaging |
Het |
| Depdc5 |
A |
G |
5: 33,136,758 (GRCm39) |
T1343A |
probably damaging |
Het |
| Eed |
A |
T |
7: 89,621,513 (GRCm39) |
L45M |
probably damaging |
Het |
| Ep300 |
T |
A |
15: 81,524,224 (GRCm39) |
S1351T |
unknown |
Het |
| Fam184b |
T |
A |
5: 45,730,604 (GRCm39) |
Q476L |
probably benign |
Het |
| Gm10722 |
A |
C |
9: 3,001,041 (GRCm39) |
Y39S |
probably benign |
Het |
| Herc1 |
A |
T |
9: 66,377,608 (GRCm39) |
K3458M |
possibly damaging |
Het |
| Ift122 |
A |
G |
6: 115,841,333 (GRCm39) |
D39G |
probably benign |
Het |
| Igf2bp1 |
A |
G |
11: 95,864,832 (GRCm39) |
Y206H |
probably damaging |
Het |
| Ighv1-19 |
T |
C |
12: 114,672,686 (GRCm39) |
I6V |
probably benign |
Het |
| Itm2c |
T |
C |
1: 85,833,059 (GRCm39) |
I131T |
probably damaging |
Het |
| Kcnd3 |
A |
T |
3: 105,566,070 (GRCm39) |
D417V |
probably damaging |
Het |
| Klf4 |
T |
C |
4: 55,530,970 (GRCm39) |
E38G |
probably damaging |
Het |
| Klk14 |
G |
A |
7: 43,341,501 (GRCm39) |
C51Y |
probably damaging |
Het |
| Lct |
T |
C |
1: 128,228,302 (GRCm39) |
M1064V |
probably benign |
Het |
| Map4 |
C |
T |
9: 109,867,157 (GRCm39) |
Q265* |
probably null |
Het |
| Mcf2l |
T |
G |
8: 13,061,808 (GRCm39) |
V893G |
probably damaging |
Het |
| Mlst8 |
C |
T |
17: 24,696,193 (GRCm39) |
D179N |
possibly damaging |
Het |
| Mup6 |
T |
A |
4: 59,964,352 (GRCm39) |
N18K |
probably damaging |
Het |
| Nbeal2 |
G |
A |
9: 110,466,531 (GRCm39) |
R764W |
probably damaging |
Het |
| Ncoa6 |
A |
T |
2: 155,248,869 (GRCm39) |
S1478R |
probably benign |
Het |
| Sacm1l |
A |
G |
9: 123,411,393 (GRCm39) |
D394G |
probably damaging |
Het |
| Schip1 |
A |
G |
3: 68,402,585 (GRCm39) |
T221A |
probably benign |
Het |
| Slc35c1 |
A |
G |
2: 92,289,366 (GRCm39) |
Y47H |
possibly damaging |
Het |
| Tspan32 |
A |
G |
7: 142,568,715 (GRCm39) |
D70G |
probably damaging |
Het |
| Vmn2r68 |
T |
C |
7: 84,882,942 (GRCm39) |
Y270C |
possibly damaging |
Het |
| Zfp777 |
A |
G |
6: 48,019,061 (GRCm39) |
V291A |
probably damaging |
Het |
|
| Other mutations in Pcdhga1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
BB009:Pcdhga1
|
UTSW |
18 |
37,796,513 (GRCm39) |
missense |
probably damaging |
1.00 |
|
BB019:Pcdhga1
|
UTSW |
18 |
37,796,513 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1074:Pcdhga1
|
UTSW |
18 |
37,958,140 (GRCm39) |
splice site |
probably benign |
|
|
R1869:Pcdhga1
|
UTSW |
18 |
37,973,143 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1871:Pcdhga1
|
UTSW |
18 |
37,973,143 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3723:Pcdhga1
|
UTSW |
18 |
37,796,045 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R3732:Pcdhga1
|
UTSW |
18 |
37,797,176 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4243:Pcdhga1
|
UTSW |
18 |
37,796,605 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4245:Pcdhga1
|
UTSW |
18 |
37,796,605 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4424:Pcdhga1
|
UTSW |
18 |
37,795,632 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R4898:Pcdhga1
|
UTSW |
18 |
37,795,407 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R4941:Pcdhga1
|
UTSW |
18 |
37,795,659 (GRCm39) |
missense |
probably benign |
0.10 |
|
R5765:Pcdhga1
|
UTSW |
18 |
37,796,714 (GRCm39) |
missense |
probably benign |
0.31 |
|
R6176:Pcdhga1
|
UTSW |
18 |
37,797,282 (GRCm39) |
missense |
probably benign |
0.22 |
|
R6380:Pcdhga1
|
UTSW |
18 |
37,796,022 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7062:Pcdhga1
|
UTSW |
18 |
37,958,130 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7146:Pcdhga1
|
UTSW |
18 |
37,795,164 (GRCm39) |
missense |
probably benign |
0.04 |
|
R7266:Pcdhga1
|
UTSW |
18 |
37,973,028 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7525:Pcdhga1
|
UTSW |
18 |
37,795,281 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7553:Pcdhga1
|
UTSW |
18 |
37,882,735 (GRCm39) |
splice site |
probably null |
|
|
R7581:Pcdhga1
|
UTSW |
18 |
37,795,230 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7932:Pcdhga1
|
UTSW |
18 |
37,796,513 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8330:Pcdhga1
|
UTSW |
18 |
37,796,376 (GRCm39) |
missense |
probably benign |
0.19 |
|
R8385:Pcdhga1
|
UTSW |
18 |
37,795,149 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8549:Pcdhga1
|
UTSW |
18 |
37,966,386 (GRCm39) |
makesense |
probably null |
|
|
R9147:Pcdhga1
|
UTSW |
18 |
37,796,433 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R9148:Pcdhga1
|
UTSW |
18 |
37,796,433 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R9192:Pcdhga1
|
UTSW |
18 |
37,973,084 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9336:Pcdhga1
|
UTSW |
18 |
37,795,251 (GRCm39) |
missense |
probably damaging |
0.97 |
|
| Predicted Primers |
PCR Primer
(F):5'- TACTGATGGCTCCACTGGTGTG -3'
(R):5'- ATGCAGGAGACTACAGCCAC -3'
Sequencing Primer
(F):5'- TGGAGCTAGCACCTCGATCTG -3'
(R):5'- CCAGGTAGAGTGTCAGGTCTGAATC -3'
|
| Posted On |
2016-06-06 |
Incidental Mutation