Incidental Mutation 'R6155:Pcdhga4'
| ID |
489552 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
044302-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.132)
|
| Stock # |
R6155 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 37819546 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Threonine
at position 365
(I365T)
|
| 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: I365T
PolyPhen 2
Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: I365T
| 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: ENSMUST00000195163
|
| 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 |
|
| Meta Mutation Damage Score |
0.1677 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.9%
- 20x: 94.1%
|
| Validation Efficiency |
|
| 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 |
|---|
| Abcg3 |
T |
C |
5: 105,111,510 (GRCm39) |
Y319C |
probably benign |
Het |
| Actn4 |
A |
C |
7: 28,595,566 (GRCm39) |
I763S |
probably damaging |
Het |
| Actr8 |
G |
A |
14: 29,700,546 (GRCm39) |
|
probably null |
Het |
| Adrb1 |
T |
C |
19: 56,711,336 (GRCm39) |
L178P |
probably damaging |
Het |
| Afap1 |
A |
G |
5: 36,092,953 (GRCm39) |
Y19C |
unknown |
Het |
| Ankrd36 |
A |
G |
11: 5,637,442 (GRCm39) |
E1337G |
probably benign |
Het |
| Arl4a |
A |
C |
12: 40,086,519 (GRCm39) |
V76G |
probably damaging |
Het |
| Bmp1 |
A |
T |
14: 70,745,447 (GRCm39) |
I246K |
probably damaging |
Het |
| Camk4 |
A |
T |
18: 33,072,500 (GRCm39) |
T18S |
unknown |
Het |
| Cep152 |
T |
C |
2: 125,423,620 (GRCm39) |
H927R |
probably benign |
Het |
| Clca3a2 |
A |
G |
3: 144,525,118 (GRCm39) |
I38T |
probably damaging |
Het |
| Clec2g |
A |
C |
6: 128,957,236 (GRCm39) |
T54P |
probably damaging |
Het |
| Cox20 |
A |
G |
1: 178,149,362 (GRCm39) |
E31G |
possibly damaging |
Het |
| Crispld1 |
T |
A |
1: 17,823,241 (GRCm39) |
H407Q |
probably benign |
Het |
| Csmd1 |
T |
C |
8: 15,953,231 (GRCm39) |
I3417V |
probably benign |
Het |
| Dhtkd1 |
A |
C |
2: 5,915,170 (GRCm39) |
H700Q |
probably null |
Het |
| Dnah10 |
G |
A |
5: 124,847,663 (GRCm39) |
V1516M |
probably damaging |
Het |
| Dnah10 |
A |
G |
5: 124,862,239 (GRCm39) |
T2165A |
probably damaging |
Het |
| Dock2 |
C |
G |
11: 34,244,123 (GRCm39) |
M1072I |
probably benign |
Het |
| F11 |
T |
A |
8: 45,705,119 (GRCm39) |
T141S |
probably damaging |
Het |
| Gabra6 |
T |
A |
11: 42,207,350 (GRCm39) |
I245F |
probably damaging |
Het |
| H2-T5 |
G |
A |
17: 36,478,399 (GRCm39) |
A211V |
possibly damaging |
Het |
| Herc1 |
T |
A |
9: 66,340,705 (GRCm39) |
C1685S |
possibly damaging |
Het |
| Iftap |
A |
T |
2: 101,406,355 (GRCm39) |
|
probably null |
Het |
| Il20 |
G |
T |
1: 130,838,477 (GRCm39) |
D73E |
probably damaging |
Het |
| Ireb2 |
C |
A |
9: 54,793,811 (GRCm39) |
P247Q |
probably damaging |
Het |
| Kcng3 |
T |
C |
17: 83,895,807 (GRCm39) |
I220V |
probably benign |
Het |
| Lce1j |
T |
G |
3: 92,696,379 (GRCm39) |
Q133P |
unknown |
Het |
| Lgals9 |
C |
T |
11: 78,854,331 (GRCm39) |
A287T |
probably benign |
Het |
| Lrrc52 |
A |
G |
1: 167,294,296 (GRCm39) |
|
probably benign |
Het |
| Map3k5 |
A |
T |
10: 19,994,187 (GRCm39) |
H1027L |
probably benign |
Het |
| Morc3 |
A |
G |
16: 93,659,313 (GRCm39) |
D407G |
possibly damaging |
Het |
| Myom1 |
T |
C |
17: 71,415,690 (GRCm39) |
|
probably null |
Het |
| Ncapg2 |
T |
C |
12: 116,401,631 (GRCm39) |
F673S |
possibly damaging |
Het |
| Ncoa6 |
T |
C |
2: 155,249,368 (GRCm39) |
D1312G |
probably damaging |
Het |
| Nkx1-1 |
A |
T |
5: 33,588,395 (GRCm39) |
F298I |
probably damaging |
Het |
| Npas2 |
G |
A |
1: 39,326,557 (GRCm39) |
R14Q |
probably damaging |
Het |
| Npas4 |
C |
T |
19: 5,036,898 (GRCm39) |
C422Y |
probably damaging |
Het |
| Or11h4 |
T |
C |
14: 50,974,076 (GRCm39) |
D181G |
probably benign |
Het |
| Or2y11 |
T |
A |
11: 49,443,411 (GRCm39) |
I279N |
possibly damaging |
Het |
| Or4c123 |
A |
G |
2: 89,126,765 (GRCm39) |
L283S |
probably damaging |
Het |
| Or5p4 |
T |
C |
7: 107,680,493 (GRCm39) |
V164A |
probably benign |
Het |
| Pear1 |
T |
A |
3: 87,666,875 (GRCm39) |
T37S |
probably damaging |
Het |
| Pkn2 |
A |
T |
3: 142,559,454 (GRCm39) |
F24I |
probably benign |
Het |
| Plcb3 |
G |
A |
19: 6,943,533 (GRCm39) |
A122V |
probably damaging |
Het |
| Pnliprp1 |
T |
C |
19: 58,718,565 (GRCm39) |
|
probably null |
Het |
| Pramel28 |
T |
A |
4: 143,691,712 (GRCm39) |
H337L |
probably benign |
Het |
| Psmb3 |
T |
A |
11: 97,603,278 (GRCm39) |
F164I |
probably damaging |
Het |
| Ptch2 |
T |
A |
4: 116,954,105 (GRCm39) |
F45Y |
probably damaging |
Het |
| Ptpn23 |
C |
A |
9: 110,216,849 (GRCm39) |
|
probably benign |
Het |
| Pusl1 |
A |
G |
4: 155,975,005 (GRCm39) |
S199P |
probably damaging |
Het |
| Rasgrp2 |
C |
A |
19: 6,452,531 (GRCm39) |
L35I |
probably damaging |
Het |
| Rictor |
T |
C |
15: 6,823,458 (GRCm39) |
L1545P |
probably benign |
Het |
| Rtn4r |
A |
T |
16: 17,969,258 (GRCm39) |
M229L |
probably benign |
Het |
| Ruvbl1 |
A |
T |
6: 88,456,107 (GRCm39) |
|
probably null |
Het |
| Slc35b3 |
A |
T |
13: 39,128,572 (GRCm39) |
S30T |
probably damaging |
Het |
| Sorcs3 |
T |
C |
19: 48,387,136 (GRCm39) |
V207A |
possibly damaging |
Het |
| Sox13 |
A |
G |
1: 133,321,005 (GRCm39) |
S2P |
probably damaging |
Het |
| Sptbn1 |
A |
C |
11: 30,087,403 (GRCm39) |
L999R |
probably damaging |
Het |
| Taf4 |
A |
G |
2: 179,555,317 (GRCm39) |
V1015A |
probably damaging |
Het |
| Top3b |
T |
C |
16: 16,709,373 (GRCm39) |
L687P |
probably damaging |
Het |
| Tpp2 |
T |
A |
1: 43,995,649 (GRCm39) |
V268E |
probably damaging |
Het |
| Ttc6 |
T |
C |
12: 57,784,402 (GRCm39) |
Y1824H |
possibly damaging |
Het |
| Txk |
A |
G |
5: 72,858,069 (GRCm39) |
Y360H |
probably damaging |
Het |
| Vmn2r57 |
T |
C |
7: 41,078,114 (GRCm39) |
I115V |
probably benign |
Het |
| Vmn2r98 |
T |
C |
17: 19,286,143 (GRCm39) |
S214P |
possibly damaging |
Het |
| Zbtb48 |
T |
C |
4: 152,106,495 (GRCm39) |
|
probably null |
Het |
| Zzz3 |
A |
G |
3: 152,133,319 (GRCm39) |
I126V |
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 |
|
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 |
|
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'- ACTGGGGACATTACAGTGTTG -3'
(R):5'- CTGTAGACAGAGGTGGAGTTC -3'
Sequencing Primer
(F):5'- ACATTACAGTGTTGGGGGAACTG -3'
(R):5'- ACAGAGGTGGAGTTCCCTGG -3'
|
| Posted On |
2017-10-10 |
Incidental Mutation