Incidental Mutation 'R7132:Pcdhga4'
| ID |
552780 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
045217-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.132)
|
| Stock # |
R7132 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 37820430 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Proline
at position 660
(T660P)
|
| 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 |
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: T660P
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: T660P
| 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 |
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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
| 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: 71 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ank3 |
C |
T |
10: 69,825,744 (GRCm39) |
A1471V |
|
Het |
| Ankrd12 |
C |
A |
17: 66,290,242 (GRCm39) |
M1730I |
probably benign |
Het |
| Ap2a2 |
T |
C |
7: 141,199,478 (GRCm39) |
Y462H |
probably benign |
Het |
| Ap5b1 |
T |
A |
19: 5,619,412 (GRCm39) |
Y277* |
probably null |
Het |
| App |
T |
C |
16: 84,853,370 (GRCm39) |
D236G |
unknown |
Het |
| Arid2 |
A |
T |
15: 96,247,894 (GRCm39) |
K102I |
possibly damaging |
Het |
| Asl |
A |
G |
5: 130,043,543 (GRCm39) |
V211A |
possibly damaging |
Het |
| Card6 |
TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG |
TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG |
15: 5,128,173 (GRCm39) |
|
probably benign |
Het |
| Cbx2 |
A |
G |
11: 118,913,947 (GRCm39) |
S5G |
probably benign |
Het |
| Ccdc183 |
A |
G |
2: 25,506,542 (GRCm39) |
|
probably null |
Het |
| Cd72 |
T |
C |
4: 43,452,444 (GRCm39) |
Q183R |
possibly damaging |
Het |
| Cdh26 |
T |
A |
2: 178,128,555 (GRCm39) |
D702E |
possibly damaging |
Het |
| Cfap61 |
A |
T |
2: 145,951,870 (GRCm39) |
N784I |
probably damaging |
Het |
| Cgrrf1 |
G |
A |
14: 47,091,321 (GRCm39) |
V282M |
probably damaging |
Het |
| Cmtm1 |
CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT |
CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT |
8: 105,036,102 (GRCm39) |
|
probably benign |
Het |
| Cobll1 |
T |
G |
2: 64,964,112 (GRCm39) |
K170Q |
probably damaging |
Het |
| Copg2 |
A |
T |
6: 30,792,931 (GRCm39) |
V468D |
probably benign |
Het |
| Cracr2b |
C |
T |
7: 141,043,651 (GRCm39) |
A84V |
probably benign |
Het |
| Cyp2f2 |
A |
T |
7: 26,831,993 (GRCm39) |
D416V |
probably benign |
Het |
| Dcaf10 |
T |
C |
4: 45,342,391 (GRCm39) |
F75S |
probably benign |
Het |
| Eml3 |
G |
T |
19: 8,918,392 (GRCm39) |
A829S |
probably benign |
Het |
| Entpd3 |
A |
G |
9: 120,390,086 (GRCm39) |
T402A |
probably benign |
Het |
| Fer1l4 |
A |
T |
2: 155,887,546 (GRCm39) |
V550E |
probably damaging |
Het |
| Fgb |
G |
A |
3: 82,954,053 (GRCm39) |
R62* |
probably null |
Het |
| Fubp1 |
T |
A |
3: 151,937,661 (GRCm39) |
|
probably null |
Het |
| Gdf3 |
A |
C |
6: 122,583,283 (GRCm39) |
D361E |
probably damaging |
Het |
| Gm6685 |
A |
T |
11: 28,289,330 (GRCm39) |
I162N |
probably damaging |
Het |
| Hmx2 |
A |
G |
7: 131,157,645 (GRCm39) |
Y253C |
probably damaging |
Het |
| Ints2 |
G |
T |
11: 86,108,580 (GRCm39) |
N922K |
probably benign |
Het |
| Ipo7 |
C |
T |
7: 109,653,254 (GRCm39) |
L984F |
probably benign |
Het |
| Itgae |
A |
T |
11: 73,002,184 (GRCm39) |
Y96F |
possibly damaging |
Het |
| Kalrn |
A |
G |
16: 34,076,597 (GRCm39) |
V697A |
unknown |
Het |
| Kctd18 |
G |
A |
1: 58,006,737 (GRCm39) |
R38* |
probably null |
Het |
| Kdm5b |
A |
G |
1: 134,526,844 (GRCm39) |
D322G |
probably damaging |
Het |
| Ldb3 |
A |
G |
14: 34,298,992 (GRCm39) |
Y211H |
probably benign |
Het |
| Limch1 |
T |
C |
5: 67,111,028 (GRCm39) |
F85S |
probably damaging |
Het |
| Lrrn4 |
A |
T |
2: 132,721,613 (GRCm39) |
L68* |
probably null |
Het |
| Lrwd1 |
A |
G |
5: 136,152,129 (GRCm39) |
V616A |
possibly damaging |
Het |
| Nars1 |
A |
G |
18: 64,640,841 (GRCm39) |
|
probably null |
Het |
| Nradd |
T |
C |
9: 110,451,329 (GRCm39) |
D13G |
probably benign |
Het |
| Oacyl |
A |
T |
18: 65,831,480 (GRCm39) |
N39I |
probably damaging |
Het |
| Onecut2 |
A |
T |
18: 64,473,983 (GRCm39) |
H178L |
possibly damaging |
Het |
| Or9i14 |
T |
A |
19: 13,792,786 (GRCm39) |
Q56L |
probably benign |
Het |
| Peg10 |
CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG |
CCACATCAGGATCCACATCAGGATGCACATCAG |
6: 4,756,398 (GRCm39) |
|
probably benign |
Het |
| Pitpnm3 |
T |
A |
11: 71,942,102 (GRCm39) |
I902F |
possibly damaging |
Het |
| Plod3 |
T |
C |
5: 137,023,971 (GRCm39) |
L180S |
|
Het |
| Prrc2c |
A |
T |
1: 162,508,850 (GRCm39) |
H2354Q |
possibly damaging |
Het |
| Pth2r |
A |
G |
1: 65,361,225 (GRCm39) |
E58G |
probably benign |
Het |
| Rev1 |
G |
T |
1: 38,110,530 (GRCm39) |
D573E |
possibly damaging |
Het |
| Sec24a |
A |
T |
11: 51,605,963 (GRCm39) |
L696* |
probably null |
Het |
| Serpinb3c |
A |
G |
1: 107,204,681 (GRCm39) |
S22P |
probably damaging |
Het |
| St18 |
A |
T |
1: 6,929,351 (GRCm39) |
H81L |
|
Het |
| Stard9 |
A |
T |
2: 120,509,859 (GRCm39) |
K266* |
probably null |
Het |
| Stip1 |
C |
T |
19: 6,999,178 (GRCm39) |
G467S |
possibly damaging |
Het |
| Syne1 |
G |
A |
10: 5,193,180 (GRCm39) |
A3956V |
probably damaging |
Het |
| Tcp10a |
C |
T |
17: 7,612,351 (GRCm39) |
T381I |
probably benign |
Het |
| Tecpr2 |
T |
A |
12: 110,881,806 (GRCm39) |
V125D |
probably damaging |
Het |
| Tmc2 |
T |
C |
2: 130,074,329 (GRCm39) |
S341P |
possibly damaging |
Het |
| Tmem190 |
G |
A |
7: 4,787,224 (GRCm39) |
V143I |
probably benign |
Het |
| Trap1 |
A |
G |
16: 3,873,693 (GRCm39) |
Y288H |
probably benign |
Het |
| Trim39 |
T |
C |
17: 36,571,547 (GRCm39) |
T404A |
probably benign |
Het |
| Ttn |
T |
A |
2: 76,576,043 (GRCm39) |
K24950I |
probably damaging |
Het |
| Ttn |
G |
T |
2: 76,774,696 (GRCm39) |
N2161K |
unknown |
Het |
| Unc13b |
T |
C |
4: 43,215,757 (GRCm39) |
S19P |
probably benign |
Het |
| Uqcrc1 |
T |
A |
9: 108,778,536 (GRCm39) |
I471N |
probably damaging |
Het |
| Wbp11 |
T |
C |
6: 136,798,540 (GRCm39) |
T170A |
probably benign |
Het |
| Wnk4 |
A |
G |
11: 101,152,026 (GRCm39) |
I177V |
probably benign |
Het |
| Zfp455 |
C |
A |
13: 67,347,230 (GRCm39) |
P51T |
probably damaging |
Het |
| Zfp946 |
T |
C |
17: 22,673,644 (GRCm39) |
Y133H |
probably benign |
Het |
| Zfp955a |
A |
T |
17: 33,460,589 (GRCm39) |
Y514* |
probably null |
Het |
| Zzef1 |
T |
C |
11: 72,808,697 (GRCm39) |
|
probably null |
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 |
|
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 |
|
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'- ATCCTGGATACCTGGTGACCAAG -3'
(R):5'- AGCCTGTGTATCAGCAGCAC -3'
Sequencing Primer
(F):5'- TGGTGGCCGTAGACAAAGACTC -3'
(R):5'- TGTGTATCAGCAGCACAATGAC -3'
|
| Posted On |
2019-05-15 |
Incidental Mutation