Incidental Mutation 'R7882:Pcdhga4'
| ID |
608845 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
045934-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.123)
|
| Stock # |
R7882 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 37819681 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 410
(D410G)
|
| 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: D410G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: D410G
| 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
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
100% (48/48) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acadm |
C |
A |
3: 153,644,250 (GRCm39) |
E110* |
probably null |
Het |
| Adad1 |
G |
T |
3: 37,133,951 (GRCm39) |
V289F |
probably damaging |
Het |
| Adgra2 |
A |
G |
8: 27,607,440 (GRCm39) |
D717G |
probably benign |
Het |
| Arid3b |
T |
C |
9: 57,703,780 (GRCm39) |
I389M |
possibly damaging |
Het |
| Axdnd1 |
A |
G |
1: 156,225,023 (GRCm39) |
V47A |
|
Het |
| Cachd1 |
T |
A |
4: 100,824,244 (GRCm39) |
L562M |
probably benign |
Het |
| Cadm2 |
A |
T |
16: 66,528,357 (GRCm39) |
I326N |
probably benign |
Het |
| Ccpg1 |
T |
C |
9: 72,922,787 (GRCm39) |
F799S |
probably damaging |
Het |
| Ces1c |
T |
C |
8: 93,833,231 (GRCm39) |
I411M |
probably benign |
Het |
| Cgn |
T |
G |
3: 94,669,941 (GRCm39) |
K1066N |
probably damaging |
Het |
| Cntn4 |
A |
G |
6: 106,330,684 (GRCm39) |
I101V |
probably benign |
Het |
| Cntrl |
A |
G |
2: 35,060,592 (GRCm39) |
E1928G |
probably benign |
Het |
| Cxcl12 |
A |
G |
6: 117,148,464 (GRCm39) |
Y28C |
probably damaging |
Het |
| Cyp2r1 |
A |
T |
7: 114,153,824 (GRCm39) |
|
probably null |
Het |
| D430041D05Rik |
C |
T |
2: 104,087,974 (GRCm39) |
W334* |
probably null |
Het |
| Dsp |
G |
A |
13: 38,367,994 (GRCm39) |
R671Q |
possibly damaging |
Het |
| Fancm |
A |
G |
12: 65,173,568 (GRCm39) |
K1960R |
probably benign |
Het |
| Fgd5 |
T |
A |
6: 92,045,459 (GRCm39) |
Y1331N |
probably damaging |
Het |
| Ina |
G |
A |
19: 47,004,100 (GRCm39) |
E303K |
|
Het |
| Kctd3 |
C |
A |
1: 188,715,243 (GRCm39) |
V369F |
possibly damaging |
Het |
| Kif14 |
T |
C |
1: 136,399,314 (GRCm39) |
|
probably null |
Het |
| Kif14 |
T |
C |
1: 136,443,763 (GRCm39) |
V1312A |
probably benign |
Het |
| Krt84 |
T |
C |
15: 101,436,826 (GRCm39) |
I403V |
probably benign |
Het |
| Krtap9-1 |
A |
C |
11: 99,764,356 (GRCm39) |
T31P |
unknown |
Het |
| Lyrm9 |
A |
T |
11: 78,728,967 (GRCm39) |
I60F |
probably damaging |
Het |
| Mast1 |
A |
G |
8: 85,639,947 (GRCm39) |
|
probably null |
Het |
| Mmp28 |
T |
C |
11: 83,334,752 (GRCm39) |
D334G |
probably damaging |
Het |
| Nr1h5 |
T |
C |
3: 102,856,931 (GRCm39) |
T194A |
possibly damaging |
Het |
| Nrf1 |
A |
G |
6: 30,090,299 (GRCm39) |
I85M |
probably benign |
Het |
| Nrp2 |
C |
T |
1: 62,822,680 (GRCm39) |
R758C |
probably damaging |
Het |
| Or5b116 |
A |
T |
19: 13,422,951 (GRCm39) |
T192S |
probably benign |
Het |
| Pld1 |
T |
C |
3: 28,099,158 (GRCm39) |
V275A |
probably damaging |
Het |
| Plxnc1 |
A |
T |
10: 94,679,698 (GRCm39) |
F895I |
probably benign |
Het |
| Polr2a |
A |
G |
11: 69,627,000 (GRCm39) |
I1486T |
possibly damaging |
Het |
| Ptprz1 |
A |
G |
6: 23,002,256 (GRCm39) |
M1449V |
probably benign |
Het |
| Rspo4 |
C |
A |
2: 151,711,746 (GRCm39) |
T156N |
probably damaging |
Het |
| Sacs |
A |
G |
14: 61,444,520 (GRCm39) |
I2189V |
probably benign |
Het |
| Stat5b |
A |
C |
11: 100,674,601 (GRCm39) |
F711V |
possibly damaging |
Het |
| Stk11ip |
C |
A |
1: 75,506,108 (GRCm39) |
Q543K |
probably benign |
Het |
| Tarbp1 |
G |
A |
8: 127,183,232 (GRCm39) |
T529M |
probably damaging |
Het |
| Thada |
A |
T |
17: 84,736,624 (GRCm39) |
C886S |
possibly damaging |
Het |
| Tmem19 |
A |
G |
10: 115,179,608 (GRCm39) |
F296S |
probably benign |
Het |
| Tnfsf13b |
A |
G |
8: 10,057,078 (GRCm39) |
N79S |
not run |
Het |
| Vdac3 |
C |
A |
8: 23,069,073 (GRCm39) |
G214C |
probably damaging |
Het |
| Vmn2r18 |
A |
C |
5: 151,485,329 (GRCm39) |
F722V |
probably damaging |
Het |
| Vmn2r45 |
A |
G |
7: 8,486,409 (GRCm39) |
L293S |
possibly damaging |
Het |
| Vmn2r88 |
C |
G |
14: 51,650,503 (GRCm39) |
A72G |
probably benign |
Het |
| Xpot |
A |
G |
10: 121,454,996 (GRCm39) |
|
probably null |
Het |
| Zfp526 |
G |
A |
7: 24,920,860 (GRCm39) |
|
probably benign |
Het |
| Zfp532 |
A |
G |
18: 65,756,561 (GRCm39) |
T165A |
probably benign |
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 |
|
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 |
|
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'- GATGTAAATGACAATGCCCCGG -3'
(R):5'- AGATGGAAGCTCCTCTAGGG -3'
Sequencing Primer
(F):5'- TGACAATGCCCCGGAAGTC -3'
(R):5'- AAGCTCCTCTAGGGTTGTTTTC -3'
|
| Posted On |
2019-12-20 |
Incidental Mutation