Incidental Mutation 'R4245:Pcdhga1'
ID |
320399 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdhga1
|
Ensembl Gene |
ENSMUSG00000103144 |
Gene Name |
protocadherin gamma subfamily A, 1 |
Synonyms |
|
MMRRC Submission |
041061-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R4245 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
18 |
Chromosomal Location |
37794846-37974926 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 37796605 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 536
(D536E)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000141367
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000115661]
[ENSMUST00000194190]
[ENSMUST00000194544]
[ENSMUST00000194888]
|
AlphaFold |
Q91XZ0 |
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000097608
|
SMART Domains |
Protein: ENSMUSP00000095213 Gene: ENSMUSG00000073590
Domain | Start | End | E-Value | Type |
transmembrane domain
|
15 |
37 |
N/A |
INTRINSIC |
transmembrane domain
|
57 |
79 |
N/A |
INTRINSIC |
|
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 |
probably damaging
Transcript: ENSMUST00000194190
AA Change: D536E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000142062 Gene: ENSMUSG00000103144 AA Change: D536E
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: D536E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000141367 Gene: ENSMUSG00000103144 AA Change: D536E
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 |
0.6467 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.5%
|
Validation Efficiency |
98% (47/48) |
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: 41 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930449A18Rik |
T |
A |
3: 59,733,203 (GRCm39) |
|
noncoding transcript |
Het |
Acacb |
A |
T |
5: 114,368,845 (GRCm39) |
T1688S |
probably damaging |
Het |
Actr1b |
T |
C |
1: 36,740,911 (GRCm39) |
Y171C |
possibly damaging |
Het |
C8a |
A |
G |
4: 104,733,543 (GRCm39) |
V4A |
probably benign |
Het |
Ccdc171 |
A |
G |
4: 83,473,045 (GRCm39) |
D158G |
probably damaging |
Het |
Ccdc184 |
T |
A |
15: 98,066,750 (GRCm39) |
|
probably null |
Het |
Cdc23 |
T |
C |
18: 34,770,100 (GRCm39) |
|
probably benign |
Het |
Dnah5 |
A |
G |
15: 28,219,335 (GRCm39) |
N51S |
probably benign |
Het |
Dock10 |
T |
A |
1: 80,544,472 (GRCm39) |
E905V |
probably benign |
Het |
Eepd1 |
T |
C |
9: 25,505,920 (GRCm39) |
I460T |
probably benign |
Het |
Fen1 |
T |
A |
19: 10,177,731 (GRCm39) |
I238F |
probably damaging |
Het |
Fhdc1 |
C |
A |
3: 84,352,133 (GRCm39) |
V1031F |
probably benign |
Het |
Gm5493 |
A |
G |
17: 22,966,199 (GRCm39) |
E28G |
probably benign |
Het |
Jakmip2 |
A |
G |
18: 43,710,501 (GRCm39) |
V234A |
probably benign |
Het |
Map3k6 |
T |
C |
4: 132,979,258 (GRCm39) |
Y1204H |
possibly damaging |
Het |
Mpeg1 |
C |
A |
19: 12,440,272 (GRCm39) |
Q577K |
probably damaging |
Het |
Mthfd1 |
T |
C |
12: 76,348,047 (GRCm39) |
S564P |
probably damaging |
Het |
Mtmr11 |
T |
A |
3: 96,075,393 (GRCm39) |
C358S |
probably damaging |
Het |
Muc4 |
T |
C |
16: 32,753,802 (GRCm38) |
I1226T |
probably benign |
Het |
Myo18b |
G |
A |
5: 112,840,261 (GRCm39) |
H2511Y |
possibly damaging |
Het |
Ndufs6 |
A |
T |
13: 73,468,512 (GRCm39) |
D62E |
probably damaging |
Het |
Or5af2 |
T |
C |
11: 58,708,604 (GRCm39) |
Y257H |
probably damaging |
Het |
Or7e178 |
T |
C |
9: 20,225,629 (GRCm39) |
I196V |
possibly damaging |
Het |
Phactr3 |
G |
A |
2: 177,924,982 (GRCm39) |
|
probably null |
Het |
Ptgir |
A |
G |
7: 16,640,794 (GRCm39) |
M29V |
possibly damaging |
Het |
Ptk2 |
C |
T |
15: 73,103,825 (GRCm39) |
G749D |
probably benign |
Het |
Rab3il1 |
A |
T |
19: 10,007,518 (GRCm39) |
D222V |
probably damaging |
Het |
Radil |
T |
C |
5: 142,529,546 (GRCm39) |
D50G |
probably damaging |
Het |
Rfx7 |
A |
G |
9: 72,499,051 (GRCm39) |
T72A |
possibly damaging |
Het |
Scn7a |
T |
C |
2: 66,572,345 (GRCm39) |
I209V |
probably benign |
Het |
Sf3a1 |
C |
T |
11: 4,117,774 (GRCm39) |
R179C |
probably damaging |
Het |
Spata31e2 |
T |
C |
1: 26,721,161 (GRCm39) |
N1340D |
probably benign |
Het |
Styxl2 |
T |
C |
1: 165,928,685 (GRCm39) |
E309G |
probably damaging |
Het |
Tg |
T |
C |
15: 66,568,318 (GRCm39) |
V1335A |
possibly damaging |
Het |
Thnsl1 |
A |
G |
2: 21,217,059 (GRCm39) |
E271G |
probably benign |
Het |
Vill |
T |
A |
9: 118,900,359 (GRCm39) |
|
probably benign |
Het |
Vmn2r79 |
A |
G |
7: 86,651,624 (GRCm39) |
D341G |
possibly damaging |
Het |
Wdr59 |
T |
C |
8: 112,216,996 (GRCm39) |
N272D |
possibly damaging |
Het |
Zar1 |
T |
C |
5: 72,737,736 (GRCm39) |
E121G |
possibly damaging |
Het |
Zfp985 |
A |
G |
4: 147,667,396 (GRCm39) |
K88R |
probably damaging |
Het |
Zscan29 |
C |
T |
2: 120,995,275 (GRCm39) |
|
probably null |
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 |
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 |
R5021:Pcdhga1
|
UTSW |
18 |
37,796,876 (GRCm39) |
missense |
probably damaging |
1.00 |
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'- TCTTCTCAGTAAAGGCCCAGG -3'
(R):5'- AGCCAAGAGTTTTGTCCTGAGTC -3'
Sequencing Primer
(F):5'- TAAAGGCCCAGGATGCTGACC -3'
(R):5'- GAGTCTTTGTCCACTGCTACCAC -3'
|
Posted On |
2015-06-12 |