Incidental Mutation 'R6936:Pcdhga4'
ID |
540319 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdhga4
|
Ensembl Gene |
ENSMUSG00000103677 |
Gene Name |
protocadherin gamma subfamily A, 4 |
Synonyms |
|
MMRRC Submission |
045050-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.123)
|
Stock # |
R6936 (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 37820458 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Glycine
at position 669
(D669G)
|
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 |
possibly damaging
Transcript: ENSMUST00000194418
AA Change: D669G
PolyPhen 2
Score 0.844 (Sensitivity: 0.83; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000142140 Gene: ENSMUSG00000103677 AA Change: D669G
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 |
|
Meta Mutation Damage Score |
0.0683 |
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.8%
- 10x: 99.0%
- 20x: 96.7%
|
Validation Efficiency |
98% (48/49) |
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: 49 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca13 |
A |
T |
11: 9,248,568 (GRCm39) |
I2772F |
probably damaging |
Het |
Adam1a |
A |
G |
5: 121,657,425 (GRCm39) |
C623R |
probably damaging |
Het |
Ak2 |
T |
C |
4: 128,893,005 (GRCm39) |
S55P |
probably damaging |
Het |
Ak4 |
C |
T |
4: 101,304,456 (GRCm39) |
A82V |
probably benign |
Het |
Arhgap10 |
A |
T |
8: 78,037,376 (GRCm39) |
C617* |
probably null |
Het |
Art1 |
A |
T |
7: 101,755,977 (GRCm39) |
D56V |
possibly damaging |
Het |
Ascc3 |
A |
G |
10: 50,606,057 (GRCm39) |
D1392G |
probably damaging |
Het |
Bbs5 |
T |
C |
2: 69,484,698 (GRCm39) |
S123P |
probably damaging |
Het |
Cabin1 |
A |
T |
10: 75,551,592 (GRCm39) |
|
probably null |
Het |
Carmil3 |
G |
A |
14: 55,739,018 (GRCm39) |
E891K |
probably benign |
Het |
Cbfa2t3 |
C |
G |
8: 123,374,478 (GRCm39) |
R89P |
probably damaging |
Het |
Ccdc157 |
A |
G |
11: 4,094,030 (GRCm39) |
S534P |
probably benign |
Het |
Cep72 |
A |
T |
13: 74,188,206 (GRCm39) |
I229N |
probably damaging |
Het |
Cnn3 |
C |
T |
3: 121,243,702 (GRCm39) |
|
probably benign |
Het |
Cyp2c70 |
A |
G |
19: 40,156,007 (GRCm39) |
V181A |
probably damaging |
Het |
Cyp2d26 |
C |
T |
15: 82,676,741 (GRCm39) |
D202N |
probably benign |
Het |
Dbh |
A |
G |
2: 27,062,809 (GRCm39) |
K343E |
probably benign |
Het |
Dlx5 |
A |
G |
6: 6,879,585 (GRCm39) |
Y161H |
probably damaging |
Het |
Dnah5 |
A |
T |
15: 28,409,414 (GRCm39) |
I3611F |
probably damaging |
Het |
Egf |
A |
C |
3: 129,474,853 (GRCm39) |
F563V |
possibly damaging |
Het |
Enpp1 |
T |
C |
10: 24,527,237 (GRCm39) |
H650R |
probably benign |
Het |
Exoc6 |
A |
G |
19: 37,560,311 (GRCm39) |
I109M |
probably benign |
Het |
Fan1 |
T |
A |
7: 64,022,234 (GRCm39) |
N340Y |
probably damaging |
Het |
Fgg |
C |
T |
3: 82,915,727 (GRCm39) |
S56F |
possibly damaging |
Het |
Fras1 |
A |
G |
5: 96,916,211 (GRCm39) |
D3415G |
possibly damaging |
Het |
Ghsr |
A |
G |
3: 27,426,474 (GRCm39) |
I177V |
probably benign |
Het |
Gm1979 |
A |
T |
5: 26,207,028 (GRCm39) |
H62Q |
probably benign |
Het |
Gpatch2 |
A |
G |
1: 186,965,433 (GRCm39) |
D313G |
probably benign |
Het |
Gtf2i |
C |
T |
5: 134,271,639 (GRCm39) |
E823K |
probably damaging |
Het |
Hook2 |
C |
A |
8: 85,729,627 (GRCm39) |
T689N |
probably benign |
Het |
Hrnr |
A |
T |
3: 93,239,667 (GRCm39) |
N3302Y |
unknown |
Het |
Igkv7-33 |
G |
A |
6: 70,035,785 (GRCm39) |
P66S |
possibly damaging |
Het |
Kcnh2 |
T |
A |
5: 24,529,337 (GRCm39) |
I800F |
probably damaging |
Het |
Mcmbp |
G |
A |
7: 128,326,920 (GRCm39) |
Q21* |
probably null |
Het |
Mmp21 |
T |
C |
7: 133,280,704 (GRCm39) |
K89E |
probably benign |
Het |
Or4b13 |
A |
G |
2: 90,082,678 (GRCm39) |
V218A |
probably benign |
Het |
Or52r1c |
A |
T |
7: 102,735,021 (GRCm39) |
I94F |
probably damaging |
Het |
Ralgapa1 |
T |
C |
12: 55,832,997 (GRCm39) |
T169A |
probably damaging |
Het |
Sec31a |
T |
C |
5: 100,540,369 (GRCm39) |
N35S |
probably benign |
Het |
Serpinb5 |
A |
T |
1: 106,798,148 (GRCm39) |
T46S |
probably benign |
Het |
Svs5 |
A |
G |
2: 164,079,548 (GRCm39) |
S120P |
possibly damaging |
Het |
Tbpl2 |
T |
C |
2: 23,984,953 (GRCm39) |
T64A |
probably benign |
Het |
Tecpr2 |
T |
A |
12: 110,911,297 (GRCm39) |
H1111Q |
possibly damaging |
Het |
Tm9sf3 |
A |
G |
19: 41,211,638 (GRCm39) |
F402L |
probably benign |
Het |
Tmem120b |
T |
G |
5: 123,254,287 (GRCm39) |
V287G |
possibly damaging |
Het |
Tmem150c |
T |
C |
5: 100,231,577 (GRCm39) |
T133A |
possibly damaging |
Het |
Ubqln3 |
A |
T |
7: 103,791,517 (GRCm39) |
V191D |
probably damaging |
Het |
Ubr2 |
T |
C |
17: 47,283,957 (GRCm39) |
E564G |
possibly damaging |
Het |
Zkscan1 |
T |
C |
5: 138,091,567 (GRCm39) |
V100A |
probably 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 |
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 |
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'- TGGCCGTAGACAAAGACTCAG -3'
(R):5'- ATTACCTGCAGCCTGAAGC -3'
Sequencing Primer
(F):5'- AGAACGCCTGGCTGTCCTAC -3'
(R):5'- CCTGAAGCAGGCGAGTTG -3'
|
Posted On |
2018-11-06 |