Incidental Mutation 'R5373:Pcdhga4'
| ID |
428901 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
042949-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.123)
|
| Stock # |
R5373 (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]
[ENSMUST00000194190]
[ENSMUST00000194418]
[ENSMUST00000194544]
[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 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 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: 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% (74/77) |
| 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: 68 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
A |
G |
3: 137,773,396 (GRCm39) |
S862G |
probably benign |
Het |
| Abcb5 |
G |
T |
12: 118,850,912 (GRCm39) |
T887K |
probably damaging |
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 |
| Arpp21 |
T |
G |
9: 111,896,336 (GRCm39) |
M687L |
probably benign |
Het |
| Camkv |
T |
C |
9: 107,824,088 (GRCm39) |
S221P |
probably benign |
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 |
| Chsy1 |
C |
T |
7: 65,759,824 (GRCm39) |
Q56* |
probably null |
Het |
| Cisd2 |
A |
G |
3: 135,114,596 (GRCm39) |
V125A |
probably benign |
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 |
| 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 |
| Dnajc6 |
T |
C |
4: 101,472,824 (GRCm39) |
I317T |
probably 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 |
| Eml2 |
A |
T |
7: 18,913,188 (GRCm39) |
D62V |
possibly damaging |
Het |
| Epb41l3 |
C |
A |
17: 69,593,795 (GRCm39) |
H810N |
probably damaging |
Het |
| Evc2 |
C |
T |
5: 37,535,554 (GRCm39) |
R410W |
probably damaging |
Het |
| Fam169b |
T |
C |
7: 67,950,586 (GRCm39) |
Y13H |
probably damaging |
Het |
| Fcrl5 |
A |
G |
3: 87,353,698 (GRCm39) |
T348A |
probably benign |
Het |
| Fezf2 |
A |
T |
14: 12,344,803 (GRCm38) |
V128E |
possibly damaging |
Het |
| Ighv3-5 |
A |
G |
12: 114,226,573 (GRCm39) |
S18P |
probably damaging |
Het |
| Kcnq5 |
T |
A |
1: 22,031,795 (GRCm39) |
H4L |
unknown |
Het |
| Kdm5d |
C |
T |
Y: 927,995 (GRCm39) |
P756S |
probably benign |
Het |
| Lig1 |
AG |
A |
7: 13,039,849 (GRCm39) |
|
probably null |
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 |
| Mtfr2 |
G |
T |
10: 20,228,598 (GRCm39) |
C48F |
probably benign |
Het |
| Nt5c |
G |
A |
11: 115,381,643 (GRCm39) |
|
probably null |
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 |
| Ptpn14 |
T |
C |
1: 189,583,160 (GRCm39) |
M669T |
probably benign |
Het |
| Ptprf |
G |
T |
4: 118,083,238 (GRCm39) |
T923K |
possibly damaging |
Het |
| Ptprg |
A |
G |
14: 12,213,665 (GRCm38) |
N1011S |
probably benign |
Het |
| Ptprz1 |
T |
A |
6: 23,007,354 (GRCm39) |
V1639E |
probably damaging |
Het |
| Rgsl1 |
C |
T |
1: 153,666,053 (GRCm39) |
V986I |
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 |
| Serpina3j |
A |
G |
12: 104,280,986 (GRCm39) |
D53G |
probably damaging |
Het |
| Slc26a7 |
A |
T |
4: 14,546,447 (GRCm39) |
I294N |
probably 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 |
| Spata6 |
T |
A |
4: 111,680,031 (GRCm39) |
|
probably null |
Het |
| Stap1 |
A |
G |
5: 86,238,787 (GRCm39) |
T152A |
possibly damaging |
Het |
| Susd5 |
G |
A |
9: 113,911,653 (GRCm39) |
G188R |
probably damaging |
Het |
| Thap2 |
A |
T |
10: 115,208,744 (GRCm39) |
Y125* |
probably null |
Het |
| Tnrc18 |
G |
A |
5: 142,725,911 (GRCm39) |
R1793C |
unknown |
Het |
| Ugt1a10 |
T |
A |
1: 87,983,632 (GRCm39) |
D143E |
probably damaging |
Het |
| Vmn1r85 |
A |
T |
7: 12,818,255 (GRCm39) |
Y296* |
probably null |
Het |
| Vmn2r71 |
C |
T |
7: 85,267,750 (GRCm39) |
T68I |
possibly damaging |
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 |
| Zfp85 |
T |
C |
13: 67,897,577 (GRCm39) |
Y165C |
probably damaging |
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 |
|
R5374: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'- TGGCGGCTCCTTACAAATCAG -3'
(R):5'- TCTCTGCTGTGCTCCAAAG -3'
Sequencing Primer
(F):5'- GGCTCCTTACAAATCAGACCGC -3'
(R):5'- TCCAAAGCTGGGGGCATTATC -3'
|
| Posted On |
2016-09-06 |
Incidental Mutation