Incidental Mutation 'R5333:Pcdhga4'
| ID |
423380 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
042915-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.132)
|
| Stock # |
R5333 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 37818477 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Cysteine
at position 9
(R9C)
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000195624
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194418
AA Change: R9C
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: R9C
| 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 |
probably benign
Transcript: ENSMUST00000195163
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.5%
- 20x: 95.9%
|
| Validation Efficiency |
97% (56/58) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930505A04Rik |
C |
T |
11: 30,376,349 (GRCm39) |
V173M |
probably damaging |
Het |
| Abca14 |
T |
A |
7: 119,888,769 (GRCm39) |
Y1238* |
probably null |
Het |
| Abcb5 |
A |
T |
12: 118,831,677 (GRCm39) |
V1225D |
probably damaging |
Het |
| Arhgef15 |
A |
G |
11: 68,838,022 (GRCm39) |
|
probably benign |
Het |
| As3mt |
A |
G |
19: 46,696,635 (GRCm39) |
R58G |
probably null |
Het |
| Asap1 |
T |
G |
15: 63,999,263 (GRCm39) |
N525T |
possibly damaging |
Het |
| Bhmt2 |
A |
G |
13: 93,807,938 (GRCm39) |
V50A |
probably benign |
Het |
| Bpnt2 |
A |
C |
4: 4,767,963 (GRCm39) |
V271G |
possibly damaging |
Het |
| Ccdc180 |
A |
T |
4: 45,890,935 (GRCm39) |
I36F |
possibly damaging |
Het |
| Cd209c |
A |
G |
8: 3,994,976 (GRCm39) |
S63P |
probably damaging |
Het |
| Cdc37 |
T |
C |
9: 21,054,457 (GRCm39) |
E56G |
possibly damaging |
Het |
| Cdkal1 |
T |
C |
13: 29,510,135 (GRCm39) |
Y541C |
probably benign |
Het |
| Cenph |
G |
T |
13: 100,898,280 (GRCm39) |
H208N |
probably benign |
Het |
| Cfap65 |
A |
T |
1: 74,942,334 (GRCm39) |
L1740Q |
probably benign |
Het |
| Cfap74 |
A |
G |
4: 155,521,197 (GRCm39) |
D623G |
probably damaging |
Het |
| Ckap4 |
C |
A |
10: 84,363,474 (GRCm39) |
V530L |
probably damaging |
Het |
| Cldn13 |
A |
T |
5: 134,943,869 (GRCm39) |
N105K |
probably benign |
Het |
| Ddn |
T |
C |
15: 98,703,237 (GRCm39) |
D685G |
possibly damaging |
Het |
| Fdxr |
T |
C |
11: 115,163,084 (GRCm39) |
I70V |
probably benign |
Het |
| Fn1 |
A |
T |
1: 71,663,339 (GRCm39) |
Y1050N |
probably damaging |
Het |
| Iqcf3 |
A |
G |
9: 106,430,860 (GRCm39) |
I96T |
possibly damaging |
Het |
| Itgax |
A |
G |
7: 127,741,455 (GRCm39) |
Y822C |
probably damaging |
Het |
| Katnb1 |
A |
T |
8: 95,822,234 (GRCm39) |
I286L |
possibly damaging |
Het |
| Lrp2 |
A |
C |
2: 69,355,572 (GRCm39) |
I424R |
probably benign |
Het |
| Lrpprc |
C |
A |
17: 85,097,821 (GRCm39) |
A41S |
probably benign |
Het |
| Mast3 |
A |
G |
8: 71,236,145 (GRCm39) |
L761P |
probably benign |
Het |
| Mmp1b |
T |
C |
9: 7,384,897 (GRCm39) |
I251V |
possibly damaging |
Het |
| Mpp4 |
C |
A |
1: 59,196,600 (GRCm39) |
R44L |
probably benign |
Het |
| Nalf1 |
T |
A |
8: 9,820,762 (GRCm39) |
Q86L |
possibly damaging |
Het |
| Nkain3 |
T |
A |
4: 20,484,889 (GRCm39) |
M63L |
probably benign |
Het |
| Nup88 |
A |
C |
11: 70,835,842 (GRCm39) |
|
probably benign |
Het |
| Obscn |
A |
T |
11: 58,953,518 (GRCm39) |
C3837S |
probably damaging |
Het |
| Ogdh |
T |
G |
11: 6,302,126 (GRCm39) |
L850V |
probably damaging |
Het |
| Or4f17-ps1 |
A |
G |
2: 111,358,048 (GRCm39) |
I148V |
probably benign |
Het |
| Or5w11 |
A |
G |
2: 87,459,458 (GRCm39) |
Y217C |
probably damaging |
Het |
| Panx2 |
T |
C |
15: 88,952,742 (GRCm39) |
I411T |
possibly damaging |
Het |
| Papss1 |
T |
A |
3: 131,348,805 (GRCm39) |
M585K |
probably damaging |
Het |
| Pcbp2 |
T |
G |
15: 102,394,456 (GRCm39) |
L180R |
possibly damaging |
Het |
| Pcdha7 |
A |
T |
18: 37,107,619 (GRCm39) |
T215S |
probably benign |
Het |
| Plin4 |
A |
G |
17: 56,411,970 (GRCm39) |
V687A |
probably benign |
Het |
| Potefam1 |
A |
T |
2: 111,024,682 (GRCm39) |
Y61N |
possibly damaging |
Het |
| Psma6 |
A |
G |
12: 55,454,213 (GRCm39) |
|
probably benign |
Het |
| Rcn1 |
A |
T |
2: 105,219,471 (GRCm39) |
S241T |
probably benign |
Het |
| Scgb2b18 |
A |
T |
7: 32,872,700 (GRCm39) |
L35H |
probably damaging |
Het |
| Slc11a1 |
A |
C |
1: 74,423,304 (GRCm39) |
D385A |
probably damaging |
Het |
| Stk31 |
T |
A |
6: 49,446,086 (GRCm39) |
C930S |
probably benign |
Het |
| Syt10 |
T |
A |
15: 89,725,932 (GRCm39) |
Q14L |
probably benign |
Het |
| Tnxb |
T |
G |
17: 34,909,205 (GRCm39) |
W1578G |
probably damaging |
Het |
| Triml1 |
C |
T |
8: 43,583,327 (GRCm39) |
A425T |
possibly damaging |
Het |
| Vil1 |
G |
A |
1: 74,471,549 (GRCm39) |
V777I |
probably benign |
Het |
| Vmn1r175 |
T |
C |
7: 23,508,004 (GRCm39) |
I208V |
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 |
|
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 |
|
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'- AGTAAGACCAGGATTTCCGGAG -3'
(R):5'- TGGGTCTTACCTCTGGAGAC -3'
Sequencing Primer
(F):5'- TTTCCGGAGCACAAAGGACTG -3'
(R):5'- GTCTTACCTCTGGAGACGATGC -3'
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| Posted On |
2016-08-04 |
Incidental Mutation