Incidental Mutation 'R7263:Pcdhga4'
| ID |
564781 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
045388-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.132)
|
| Stock # |
R7263 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 37819873 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Isoleucine
at position 474
(T474I)
|
| 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 benign
Transcript: ENSMUST00000194418
AA Change: T474I
PolyPhen 2
Score 0.419 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: T474I
| 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 |
0.0872 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.4%
|
| Validation Efficiency |
96% (67/70) |
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca4 |
C |
A |
3: 121,847,843 (GRCm39) |
H55N |
probably damaging |
Het |
| Acan |
G |
T |
7: 78,742,066 (GRCm39) |
V488L |
probably damaging |
Het |
| Adam12 |
T |
C |
7: 133,521,240 (GRCm39) |
E638G |
possibly damaging |
Het |
| Adamts20 |
T |
A |
15: 94,220,772 (GRCm39) |
Q1387L |
possibly damaging |
Het |
| Adamts3 |
G |
T |
5: 89,825,601 (GRCm39) |
D1079E |
probably benign |
Het |
| Barx1 |
G |
T |
13: 48,818,555 (GRCm39) |
G93C |
probably damaging |
Het |
| Carmil2 |
C |
T |
8: 106,419,677 (GRCm39) |
R828C |
probably damaging |
Het |
| Catsper4 |
TTCTC |
TTC |
4: 133,954,423 (GRCm39) |
|
probably null |
Het |
| Ccdc159 |
T |
C |
9: 21,843,007 (GRCm39) |
M148T |
probably benign |
Het |
| Cdk5rap1 |
T |
A |
2: 154,202,652 (GRCm39) |
N193Y |
probably benign |
Het |
| Csnk1g2 |
G |
A |
10: 80,470,332 (GRCm39) |
G15D |
probably damaging |
Het |
| Dach1 |
T |
C |
14: 98,406,295 (GRCm39) |
S151G |
probably benign |
Het |
| Elf5 |
C |
A |
2: 103,269,645 (GRCm39) |
N75K |
probably benign |
Het |
| Elp3 |
T |
C |
14: 65,802,782 (GRCm39) |
D272G |
probably damaging |
Het |
| Epb41l1 |
T |
A |
2: 156,337,043 (GRCm39) |
|
probably null |
Het |
| Epha6 |
A |
G |
16: 59,596,028 (GRCm39) |
Y888H |
probably damaging |
Het |
| Fibcd1 |
T |
C |
2: 31,707,222 (GRCm39) |
Y345C |
probably damaging |
Het |
| Gjd3 |
C |
T |
11: 102,690,963 (GRCm39) |
E347K |
possibly damaging |
Het |
| Gse1 |
A |
G |
8: 121,300,910 (GRCm39) |
D892G |
unknown |
Het |
| Gtpbp6 |
A |
T |
5: 110,251,915 (GRCm39) |
I506N |
probably benign |
Het |
| Hivep1 |
T |
A |
13: 42,311,668 (GRCm39) |
F1303I |
possibly damaging |
Het |
| Il21r |
A |
G |
7: 125,232,077 (GRCm39) |
T502A |
probably benign |
Het |
| Ints1 |
T |
C |
5: 139,749,834 (GRCm39) |
T997A |
possibly damaging |
Het |
| Invs |
C |
A |
4: 48,396,381 (GRCm39) |
N351K |
probably damaging |
Het |
| Iqcm |
A |
G |
8: 76,489,701 (GRCm39) |
T390A |
probably benign |
Het |
| Iqcn |
A |
G |
8: 71,163,425 (GRCm39) |
N873D |
possibly damaging |
Het |
| Kcnh4 |
C |
T |
11: 100,632,643 (GRCm39) |
G948D |
probably benign |
Het |
| Kcnh7 |
T |
A |
2: 62,566,314 (GRCm39) |
|
probably null |
Het |
| Lrrc72 |
A |
G |
12: 36,258,611 (GRCm39) |
V82A |
probably damaging |
Het |
| Macf1 |
A |
T |
4: 123,271,943 (GRCm39) |
L6535Q |
probably damaging |
Het |
| Ncor2 |
G |
C |
5: 125,109,196 (GRCm39) |
L585V |
|
Het |
| Nipal2 |
G |
C |
15: 34,578,904 (GRCm39) |
Y298* |
probably null |
Het |
| Nipsnap1 |
C |
T |
11: 4,832,960 (GRCm39) |
|
probably benign |
Het |
| Or12e1 |
T |
A |
2: 87,022,476 (GRCm39) |
C148* |
probably null |
Het |
| Or4x12-ps1 |
T |
C |
2: 89,916,332 (GRCm39) |
I158V |
not run |
Het |
| Or51g1 |
A |
T |
7: 102,633,524 (GRCm39) |
Y282* |
probably null |
Het |
| Pdp1 |
G |
T |
4: 11,960,821 (GRCm39) |
Q516K |
possibly damaging |
Het |
| Pik3c2b |
C |
T |
1: 133,017,940 (GRCm39) |
P934L |
probably damaging |
Het |
| Pp2d1 |
A |
G |
17: 53,822,358 (GRCm39) |
I236T |
probably benign |
Het |
| Pygm |
G |
A |
19: 6,438,357 (GRCm39) |
R278H |
probably damaging |
Het |
| Rb1 |
A |
T |
14: 73,520,363 (GRCm39) |
C215* |
probably null |
Het |
| Rgs22 |
A |
G |
15: 36,015,789 (GRCm39) |
S1156P |
possibly damaging |
Het |
| Rgs9bp |
T |
C |
7: 35,284,126 (GRCm39) |
T174A |
probably damaging |
Het |
| Rnf133 |
A |
T |
6: 23,649,667 (GRCm39) |
Y130* |
probably null |
Het |
| Sctr |
G |
A |
1: 119,949,955 (GRCm39) |
R48Q |
probably benign |
Het |
| Serpinb6e |
A |
T |
13: 34,022,923 (GRCm39) |
F153L |
probably benign |
Het |
| Slc22a1 |
A |
T |
17: 12,885,587 (GRCm39) |
Y200N |
probably damaging |
Het |
| Slc22a22 |
C |
A |
15: 57,113,107 (GRCm39) |
M377I |
probably benign |
Het |
| Slc36a4 |
A |
G |
9: 15,633,452 (GRCm39) |
|
probably null |
Het |
| Slc39a6 |
A |
G |
18: 24,734,260 (GRCm39) |
V143A |
probably benign |
Het |
| Slf2 |
G |
A |
19: 44,926,863 (GRCm39) |
|
probably null |
Het |
| Sowaha |
T |
C |
11: 53,370,485 (GRCm39) |
K84E |
probably benign |
Het |
| Spef2 |
T |
G |
15: 9,653,098 (GRCm39) |
|
probably null |
Het |
| Sphkap |
A |
T |
1: 83,254,399 (GRCm39) |
F1117I |
probably damaging |
Het |
| Tas2r113 |
T |
C |
6: 132,870,539 (GRCm39) |
I189T |
possibly damaging |
Het |
| Tescl |
T |
C |
7: 24,033,247 (GRCm39) |
E26G |
possibly damaging |
Het |
| Trpm6 |
A |
T |
19: 18,854,150 (GRCm39) |
I1847F |
probably damaging |
Het |
| Uba1y |
T |
A |
Y: 822,200 (GRCm39) |
C178S |
possibly damaging |
Het |
| Ush2a |
T |
A |
1: 188,175,526 (GRCm39) |
V1208D |
possibly damaging |
Het |
| Usp13 |
G |
C |
3: 32,949,000 (GRCm39) |
A446P |
probably damaging |
Het |
| Usp7 |
A |
T |
16: 8,514,588 (GRCm39) |
C722S |
possibly damaging |
Het |
| Vmn1r52 |
A |
G |
6: 90,156,535 (GRCm39) |
S280G |
probably benign |
Het |
| Vmn2r84 |
T |
C |
10: 130,225,077 (GRCm39) |
K478E |
probably damaging |
Het |
| Zfp112 |
C |
A |
7: 23,824,952 (GRCm39) |
L311I |
probably benign |
Het |
| Zfp180 |
G |
T |
7: 23,805,125 (GRCm39) |
E515* |
probably null |
Het |
| Zfp518b |
A |
G |
5: 38,829,671 (GRCm39) |
I778T |
probably damaging |
Het |
| Zfp800 |
A |
T |
6: 28,243,662 (GRCm39) |
H434Q |
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 |
|
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'- CATCGGTTGTTGATACACAGGAC -3'
(R):5'- TGGCTGTCACCAGTAACTTC -3'
Sequencing Primer
(F):5'- TGTTGATACACAGGACTCTGGAC -3'
(R):5'- GGCTGTCACCAGTAACTTCAAGTC -3'
|
| Posted On |
2019-06-26 |
Incidental Mutation