Incidental Mutation 'R5374:Pcdhga4'
ID |
428977 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdhga4
|
Ensembl Gene |
ENSMUSG00000103677 |
Gene Name |
protocadherin gamma subfamily A, 4 |
Synonyms |
|
MMRRC Submission |
042950-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.132)
|
Stock # |
R5374 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
18 |
Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 37818649 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Alanine
at position 66
(V66A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000142140
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000073447]
[ENSMUST00000115661]
[ENSMUST00000192931]
[ENSMUST00000193869]
[ENSMUST00000194418]
[ENSMUST00000194544]
[ENSMUST00000194190]
[ENSMUST00000195112]
|
AlphaFold |
Q91XY4 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000073447
|
SMART Domains |
Protein: ENSMUSP00000073150 Gene: ENSMUSG00000104346
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
CA
|
42 |
128 |
2.15e-2 |
SMART |
CA
|
152 |
237 |
4.8e-13 |
SMART |
CA
|
261 |
342 |
9.36e-25 |
SMART |
CA
|
366 |
447 |
6.62e-25 |
SMART |
CA
|
471 |
557 |
6.72e-26 |
SMART |
CA
|
588 |
666 |
2.15e-15 |
SMART |
Pfam:Cadherin_C_2
|
685 |
768 |
4.8e-24 |
PFAM |
Pfam:Cadherin_tail
|
805 |
928 |
8.1e-38 |
PFAM |
|
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 |
probably benign
Transcript: ENSMUST00000192931
|
SMART Domains |
Protein: ENSMUSP00000141348 Gene: ENSMUSG00000103037
Domain | Start | End | E-Value | Type |
CA
|
36 |
119 |
8e-3 |
SMART |
CA
|
143 |
228 |
1.34e-20 |
SMART |
CA
|
252 |
333 |
1.52e-24 |
SMART |
CA
|
357 |
438 |
9.22e-24 |
SMART |
CA
|
462 |
548 |
1.24e-24 |
SMART |
CA
|
579 |
660 |
1.3e-9 |
SMART |
transmembrane domain
|
679 |
701 |
N/A |
INTRINSIC |
low complexity region
|
899 |
918 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000193631
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000193869
|
SMART Domains |
Protein: ENSMUSP00000141482 Gene: ENSMUSG00000103332
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
28 |
N/A |
INTRINSIC |
CA
|
45 |
131 |
1.64e-2 |
SMART |
CA
|
155 |
240 |
6.42e-23 |
SMART |
CA
|
264 |
345 |
1.76e-20 |
SMART |
CA
|
369 |
450 |
2.27e-23 |
SMART |
CA
|
474 |
560 |
1.5e-23 |
SMART |
CA
|
591 |
669 |
1.17e-16 |
SMART |
transmembrane domain
|
692 |
714 |
N/A |
INTRINSIC |
low complexity region
|
912 |
931 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000193984
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000194418
AA Change: V66A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000142140 Gene: ENSMUSG00000103677 AA Change: V66A
Domain | Start | End | E-Value | Type |
CA
|
44 |
130 |
1.64e-2 |
SMART |
CA
|
154 |
239 |
3.93e-18 |
SMART |
CA
|
263 |
344 |
5.22e-23 |
SMART |
CA
|
368 |
449 |
5.02e-25 |
SMART |
CA
|
473 |
559 |
2.07e-26 |
SMART |
CA
|
590 |
668 |
6.84e-18 |
SMART |
transmembrane domain
|
690 |
712 |
N/A |
INTRINSIC |
low complexity region
|
911 |
930 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195624
|
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 benign
Transcript: ENSMUST00000194190
|
SMART Domains |
Protein: ENSMUSP00000142062 Gene: ENSMUSG00000103144
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 |
probably benign
Transcript: ENSMUST00000195112
|
SMART Domains |
Protein: ENSMUSP00000141449 Gene: ENSMUSG00000102748
Domain | Start | End | E-Value | Type |
CA
|
24 |
130 |
8.18e-3 |
SMART |
CA
|
154 |
239 |
1.39e-18 |
SMART |
CA
|
263 |
344 |
7.91e-23 |
SMART |
CA
|
368 |
449 |
2.27e-23 |
SMART |
CA
|
473 |
559 |
1.24e-24 |
SMART |
CA
|
590 |
671 |
1.3e-9 |
SMART |
transmembrane domain
|
690 |
712 |
N/A |
INTRINSIC |
low complexity region
|
909 |
928 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000195163
|
Meta Mutation Damage Score |
0.1584 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.2%
|
Validation Efficiency |
96% (81/84) |
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]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 77 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1110002E22Rik |
A |
G |
3: 137,773,396 (GRCm39) |
S862G |
probably benign |
Het |
Adgrf1 |
G |
A |
17: 43,601,896 (GRCm39) |
|
probably benign |
Het |
Adss2 |
T |
G |
1: 177,623,954 (GRCm39) |
I3L |
probably benign |
Het |
Anapc7 |
T |
A |
5: 122,576,280 (GRCm39) |
D302E |
probably benign |
Het |
Ank3 |
A |
G |
10: 69,789,306 (GRCm39) |
|
probably null |
Het |
Astn2 |
A |
C |
4: 65,315,242 (GRCm39) |
V1145G |
probably damaging |
Het |
Babam2 |
C |
T |
5: 32,164,574 (GRCm39) |
|
probably benign |
Het |
Blvrb |
A |
G |
7: 27,165,271 (GRCm39) |
H238R |
possibly damaging |
Het |
Cacna1b |
C |
T |
2: 24,596,228 (GRCm39) |
V488I |
probably damaging |
Het |
Ccdc88a |
C |
T |
11: 29,413,409 (GRCm39) |
T649M |
possibly damaging |
Het |
Cdh12 |
A |
C |
15: 21,583,998 (GRCm39) |
S613R |
probably damaging |
Het |
Cisd2 |
A |
G |
3: 135,114,596 (GRCm39) |
V125A |
probably benign |
Het |
Clcn2 |
C |
A |
16: 20,528,419 (GRCm39) |
G478W |
possibly damaging |
Het |
Cntnap2 |
T |
A |
6: 47,084,903 (GRCm39) |
H1121Q |
probably benign |
Het |
Corin |
A |
T |
5: 72,462,296 (GRCm39) |
C876S |
probably damaging |
Het |
Cox7c |
T |
C |
13: 86,194,739 (GRCm39) |
Y19C |
probably benign |
Het |
Cplane1 |
T |
C |
15: 8,300,287 (GRCm39) |
V3198A |
unknown |
Het |
Cspp1 |
T |
G |
1: 10,204,351 (GRCm39) |
L1038R |
probably damaging |
Het |
Cwc15 |
A |
G |
9: 14,416,234 (GRCm39) |
K147E |
possibly damaging |
Het |
Dlgap2 |
A |
G |
8: 14,873,614 (GRCm39) |
D739G |
probably benign |
Het |
Dmxl2 |
A |
G |
9: 54,276,473 (GRCm39) |
|
probably benign |
Het |
Dock5 |
A |
G |
14: 68,043,205 (GRCm39) |
V864A |
possibly damaging |
Het |
Dock7 |
A |
G |
4: 98,877,275 (GRCm39) |
F1088L |
possibly damaging |
Het |
Dpysl3 |
T |
C |
18: 43,494,101 (GRCm39) |
Y193C |
probably damaging |
Het |
Dtna |
T |
C |
18: 23,784,670 (GRCm39) |
Y730H |
probably damaging |
Het |
Dusp3 |
A |
G |
11: 101,875,451 (GRCm39) |
Y38H |
possibly damaging |
Het |
Eif3m |
A |
T |
2: 104,843,277 (GRCm39) |
I151N |
probably damaging |
Het |
Entpd2 |
C |
T |
2: 25,289,738 (GRCm39) |
T380I |
probably damaging |
Het |
Epb41l3 |
C |
A |
17: 69,593,795 (GRCm39) |
H810N |
probably damaging |
Het |
Fcrl5 |
A |
G |
3: 87,353,698 (GRCm39) |
T348A |
probably benign |
Het |
Ginm1 |
A |
G |
10: 7,655,078 (GRCm39) |
S55P |
probably damaging |
Het |
Glt1d1 |
C |
A |
5: 127,734,148 (GRCm39) |
|
probably null |
Het |
Gm15433 |
T |
A |
1: 84,941,833 (GRCm39) |
|
noncoding transcript |
Het |
Gm8221 |
A |
G |
15: 77,510,352 (GRCm39) |
|
noncoding transcript |
Het |
Gramd1c |
A |
G |
16: 43,803,604 (GRCm39) |
V603A |
probably benign |
Het |
Grm1 |
A |
G |
10: 10,956,186 (GRCm39) |
S33P |
probably benign |
Het |
Gstp3 |
T |
C |
19: 4,107,922 (GRCm39) |
N137S |
possibly damaging |
Het |
Kdm5d |
C |
T |
Y: 927,995 (GRCm39) |
P756S |
probably benign |
Het |
Ly75 |
A |
T |
2: 60,142,115 (GRCm39) |
L1332M |
possibly damaging |
Het |
Med1 |
T |
A |
11: 98,054,789 (GRCm39) |
K378N |
probably damaging |
Het |
Mn1 |
A |
G |
5: 111,569,752 (GRCm39) |
|
probably null |
Het |
Mpo |
T |
C |
11: 87,694,437 (GRCm39) |
|
probably null |
Het |
Nom1 |
C |
G |
5: 29,646,377 (GRCm39) |
R555G |
probably damaging |
Het |
Nsmce4a |
C |
T |
7: 130,139,900 (GRCm39) |
R276Q |
probably benign |
Het |
Nt5c |
G |
A |
11: 115,381,643 (GRCm39) |
|
probably null |
Het |
Olfr908 |
CACAACAACA |
CACAACA |
9: 38,427,434 (GRCm39) |
|
probably benign |
Het |
Or52e18 |
G |
T |
7: 104,609,203 (GRCm39) |
H245Q |
probably damaging |
Het |
Or5p52 |
T |
C |
7: 107,502,698 (GRCm39) |
I258T |
possibly damaging |
Het |
Pik3c3 |
T |
C |
18: 30,445,614 (GRCm39) |
S534P |
probably benign |
Het |
Pla2g4e |
A |
T |
2: 120,016,876 (GRCm39) |
C222S |
probably benign |
Het |
Plch1 |
A |
C |
3: 63,605,499 (GRCm39) |
H1468Q |
probably benign |
Het |
Psd2 |
T |
A |
18: 36,140,556 (GRCm39) |
W610R |
probably damaging |
Het |
Ptgs1 |
A |
T |
2: 36,141,198 (GRCm39) |
K548N |
probably damaging |
Het |
Ptprz1 |
T |
A |
6: 23,007,354 (GRCm39) |
V1639E |
probably damaging |
Het |
Rangap1 |
A |
T |
15: 81,590,695 (GRCm39) |
S466T |
probably benign |
Het |
Rgsl1 |
C |
T |
1: 153,666,053 (GRCm39) |
V986I |
probably benign |
Het |
Rhobtb3 |
T |
C |
13: 76,027,014 (GRCm39) |
Y453C |
probably damaging |
Het |
Rspry1 |
T |
C |
8: 95,349,636 (GRCm39) |
V8A |
probably benign |
Het |
Rspry1 |
C |
A |
8: 95,380,892 (GRCm39) |
R399S |
probably benign |
Het |
Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
Rxfp2 |
A |
G |
5: 149,993,725 (GRCm39) |
T596A |
probably benign |
Het |
Sap18b |
G |
A |
8: 96,551,998 (GRCm39) |
A3T |
unknown |
Het |
Serpina3j |
A |
G |
12: 104,280,986 (GRCm39) |
D53G |
probably damaging |
Het |
Skint3 |
T |
A |
4: 112,155,386 (GRCm39) |
D381E |
possibly damaging |
Het |
Slirp |
T |
C |
12: 87,496,192 (GRCm39) |
S96P |
possibly damaging |
Het |
Snx6 |
T |
C |
12: 54,817,513 (GRCm39) |
E128G |
probably damaging |
Het |
Stap1 |
A |
G |
5: 86,238,787 (GRCm39) |
T152A |
possibly damaging |
Het |
Tcf20 |
A |
T |
15: 82,736,158 (GRCm39) |
N1764K |
probably damaging |
Het |
Thap2 |
A |
T |
10: 115,208,744 (GRCm39) |
Y125* |
probably null |
Het |
Ticrr |
T |
G |
7: 79,340,690 (GRCm39) |
Y1031* |
probably null |
Het |
Tnrc18 |
G |
A |
5: 142,725,911 (GRCm39) |
R1793C |
unknown |
Het |
Trpm3 |
C |
T |
19: 22,903,548 (GRCm39) |
R945* |
probably null |
Het |
Ugt1a10 |
T |
A |
1: 87,983,632 (GRCm39) |
D143E |
probably damaging |
Het |
Ush2a |
C |
T |
1: 188,487,403 (GRCm39) |
T3057M |
probably benign |
Het |
Zc3h6 |
A |
T |
2: 128,844,076 (GRCm39) |
I207F |
possibly damaging |
Het |
Zfp518a |
T |
C |
19: 40,901,954 (GRCm39) |
S628P |
probably benign |
Het |
Zup1 |
T |
C |
10: 33,803,462 (GRCm39) |
N541D |
possibly damaging |
Het |
|
Other mutations in Pcdhga4 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
PIT1430001:Pcdhga4
|
UTSW |
18 |
37,819,267 (GRCm39) |
missense |
probably benign |
0.00 |
R3828:Pcdhga4
|
UTSW |
18 |
37,820,654 (GRCm39) |
missense |
possibly damaging |
0.62 |
R3970:Pcdhga4
|
UTSW |
18 |
37,820,654 (GRCm39) |
missense |
possibly damaging |
0.62 |
R4080:Pcdhga4
|
UTSW |
18 |
37,818,832 (GRCm39) |
missense |
probably damaging |
1.00 |
R4356:Pcdhga4
|
UTSW |
18 |
37,820,664 (GRCm39) |
missense |
probably damaging |
1.00 |
R4834:Pcdhga4
|
UTSW |
18 |
37,818,490 (GRCm39) |
missense |
probably benign |
0.01 |
R4983:Pcdhga4
|
UTSW |
18 |
37,819,572 (GRCm39) |
missense |
probably damaging |
1.00 |
R5076:Pcdhga4
|
UTSW |
18 |
37,818,648 (GRCm39) |
missense |
probably benign |
0.43 |
R5186:Pcdhga4
|
UTSW |
18 |
37,820,479 (GRCm39) |
missense |
probably benign |
0.07 |
R5194:Pcdhga4
|
UTSW |
18 |
37,820,794 (GRCm39) |
missense |
probably benign |
0.08 |
R5326:Pcdhga4
|
UTSW |
18 |
37,819,651 (GRCm39) |
missense |
probably damaging |
0.98 |
R5333:Pcdhga4
|
UTSW |
18 |
37,818,477 (GRCm39) |
missense |
probably benign |
0.00 |
R5373:Pcdhga4
|
UTSW |
18 |
37,818,649 (GRCm39) |
missense |
probably damaging |
1.00 |
R5419:Pcdhga4
|
UTSW |
18 |
37,819,798 (GRCm39) |
missense |
probably damaging |
1.00 |
R5542:Pcdhga4
|
UTSW |
18 |
37,819,651 (GRCm39) |
missense |
probably damaging |
0.98 |
R5878:Pcdhga4
|
UTSW |
18 |
37,820,739 (GRCm39) |
missense |
probably benign |
0.03 |
R5996:Pcdhga4
|
UTSW |
18 |
37,818,991 (GRCm39) |
missense |
probably benign |
0.03 |
R6056:Pcdhga4
|
UTSW |
18 |
37,819,383 (GRCm39) |
missense |
probably benign |
0.00 |
R6083:Pcdhga4
|
UTSW |
18 |
37,820,478 (GRCm39) |
missense |
probably damaging |
0.98 |
R6155:Pcdhga4
|
UTSW |
18 |
37,819,546 (GRCm39) |
missense |
probably damaging |
0.98 |
R6208:Pcdhga4
|
UTSW |
18 |
37,819,762 (GRCm39) |
missense |
probably damaging |
1.00 |
R6306:Pcdhga4
|
UTSW |
18 |
37,818,966 (GRCm39) |
missense |
probably damaging |
1.00 |
R6580:Pcdhga4
|
UTSW |
18 |
37,820,370 (GRCm39) |
missense |
possibly damaging |
0.93 |
R6936:Pcdhga4
|
UTSW |
18 |
37,820,458 (GRCm39) |
missense |
possibly damaging |
0.84 |
R7132:Pcdhga4
|
UTSW |
18 |
37,820,430 (GRCm39) |
missense |
probably damaging |
1.00 |
R7159:Pcdhga4
|
UTSW |
18 |
37,819,972 (GRCm39) |
missense |
probably damaging |
1.00 |
R7257:Pcdhga4
|
UTSW |
18 |
37,820,451 (GRCm39) |
missense |
probably damaging |
0.99 |
R7263:Pcdhga4
|
UTSW |
18 |
37,819,873 (GRCm39) |
missense |
probably benign |
0.42 |
R7825:Pcdhga4
|
UTSW |
18 |
37,820,374 (GRCm39) |
missense |
probably damaging |
1.00 |
R7882:Pcdhga4
|
UTSW |
18 |
37,819,681 (GRCm39) |
missense |
probably damaging |
1.00 |
R7916:Pcdhga4
|
UTSW |
18 |
37,818,502 (GRCm39) |
missense |
probably benign |
0.22 |
R8053:Pcdhga4
|
UTSW |
18 |
37,819,308 (GRCm39) |
missense |
probably benign |
0.07 |
R9184:Pcdhga4
|
UTSW |
18 |
37,820,460 (GRCm39) |
missense |
possibly damaging |
0.95 |
R9292:Pcdhga4
|
UTSW |
18 |
37,819,713 (GRCm39) |
missense |
probably benign |
0.00 |
R9417:Pcdhga4
|
UTSW |
18 |
37,820,560 (GRCm39) |
missense |
probably damaging |
1.00 |
R9483:Pcdhga4
|
UTSW |
18 |
37,819,746 (GRCm39) |
missense |
possibly damaging |
0.73 |
R9562:Pcdhga4
|
UTSW |
18 |
37,819,527 (GRCm39) |
missense |
probably benign |
0.03 |
|
Predicted Primers |
PCR Primer
(F):5'- GGCTCCTTACAAATCAGACCGC -3'
(R):5'- CTCTCTGCTGTGCTCCAAAG -3'
Sequencing Primer
(F):5'- CAGGGGACTAATCTGGATCTGC -3'
(R):5'- TCCAAAGCTGGGGGCATTATC -3'
|
Posted On |
2016-09-06 |