Incidental Mutation 'R5194:Pcdhga4'
| ID |
400036 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
042770-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.123)
|
| Stock # |
R5194 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 37820794 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Proline
at position 781
(Q781P)
|
| 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 |
unknown
Transcript: ENSMUST00000195163
AA Change: Q253P
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194418
AA Change: Q781P
PolyPhen 2
Score 0.078 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: Q781P
| 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 |
noncoding transcript
Transcript: ENSMUST00000195624
|
| 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 |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.5%
|
| Validation Efficiency |
98% (59/60) |
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700122O11Rik |
T |
C |
17: 48,348,059 (GRCm39) |
N82D |
probably benign |
Het |
| Aadacl4fm2 |
A |
G |
4: 144,281,652 (GRCm39) |
V380A |
probably benign |
Het |
| Acadm |
C |
T |
3: 153,638,755 (GRCm39) |
R206H |
possibly damaging |
Het |
| Acly |
T |
A |
11: 100,414,372 (GRCm39) |
Y18F |
probably benign |
Het |
| Acnat2 |
G |
T |
4: 49,380,452 (GRCm39) |
Q291K |
probably benign |
Het |
| Agtpbp1 |
T |
C |
13: 59,648,453 (GRCm39) |
I456V |
probably benign |
Het |
| Ankrd7 |
A |
G |
6: 18,868,076 (GRCm39) |
N114S |
possibly damaging |
Het |
| Arfgef1 |
A |
T |
1: 10,275,132 (GRCm39) |
L307I |
probably benign |
Het |
| Arhgef2 |
A |
T |
3: 88,542,956 (GRCm39) |
I383F |
probably damaging |
Het |
| Cbs |
C |
T |
17: 31,843,198 (GRCm39) |
|
probably null |
Het |
| Cep135 |
T |
C |
5: 76,763,624 (GRCm39) |
V538A |
probably benign |
Het |
| Dennd5a |
T |
C |
7: 109,532,936 (GRCm39) |
E254G |
probably damaging |
Het |
| Drc7 |
T |
C |
8: 95,788,345 (GRCm39) |
V236A |
probably benign |
Het |
| Dtna |
C |
T |
18: 23,723,302 (GRCm39) |
Q169* |
probably null |
Het |
| Egfem1 |
G |
A |
3: 29,411,345 (GRCm39) |
|
probably null |
Het |
| Eif2ak3 |
T |
C |
6: 70,835,462 (GRCm39) |
S130P |
possibly damaging |
Het |
| Ewsr1 |
T |
C |
11: 5,032,355 (GRCm39) |
N297S |
unknown |
Het |
| F13a1 |
T |
G |
13: 37,156,037 (GRCm39) |
D192A |
probably damaging |
Het |
| Fam120a |
A |
G |
13: 49,034,411 (GRCm39) |
V1067A |
probably benign |
Het |
| Gm17490 |
T |
C |
2: 11,631,062 (GRCm39) |
Y5C |
unknown |
Het |
| Gm57859 |
T |
C |
11: 113,579,654 (GRCm39) |
S350P |
possibly damaging |
Het |
| Gm8587 |
C |
T |
12: 88,056,556 (GRCm39) |
|
noncoding transcript |
Het |
| H2-Ab1 |
C |
T |
17: 34,488,352 (GRCm39) |
|
probably benign |
Het |
| Hoxd12 |
T |
C |
2: 74,505,447 (GRCm39) |
L6P |
probably damaging |
Het |
| Ifi204 |
C |
T |
1: 173,576,910 (GRCm39) |
D564N |
possibly damaging |
Het |
| Irak2 |
T |
C |
6: 113,667,751 (GRCm39) |
V444A |
probably benign |
Het |
| Lgr6 |
C |
T |
1: 134,921,748 (GRCm39) |
A199T |
probably damaging |
Het |
| Lrba |
A |
C |
3: 86,235,526 (GRCm39) |
N877H |
probably damaging |
Het |
| Mylk3 |
T |
C |
8: 86,079,495 (GRCm39) |
I388V |
probably benign |
Het |
| Myo9b |
C |
T |
8: 71,801,733 (GRCm39) |
A1286V |
probably benign |
Het |
| Myt1l |
A |
C |
12: 29,861,647 (GRCm39) |
D143A |
unknown |
Het |
| Ngfr |
T |
C |
11: 95,471,808 (GRCm39) |
N63S |
probably benign |
Het |
| Or2ag16 |
A |
T |
7: 106,352,426 (GRCm39) |
H56Q |
probably benign |
Het |
| Or4c3 |
T |
A |
2: 89,851,870 (GRCm39) |
Y180F |
probably damaging |
Het |
| Or51a7 |
A |
G |
7: 102,615,071 (GRCm39) |
I255V |
probably benign |
Het |
| Or6c70 |
C |
T |
10: 129,709,967 (GRCm39) |
V220I |
probably benign |
Het |
| Or6z6 |
A |
G |
7: 6,491,519 (GRCm39) |
L118P |
probably damaging |
Het |
| P2rx7 |
T |
C |
5: 122,811,858 (GRCm39) |
S390P |
probably benign |
Het |
| Phip |
G |
A |
9: 82,790,915 (GRCm39) |
S677F |
probably benign |
Het |
| Ptpdc1 |
C |
A |
13: 48,740,265 (GRCm39) |
V389F |
possibly damaging |
Het |
| Rab2a |
T |
A |
4: 8,604,381 (GRCm39) |
I161N |
probably benign |
Het |
| Rnf113a2 |
T |
A |
12: 84,464,111 (GRCm39) |
M1K |
probably null |
Het |
| Schip1 |
T |
C |
3: 68,402,205 (GRCm39) |
V122A |
probably benign |
Het |
| Sdr16c5 |
C |
A |
4: 4,006,663 (GRCm39) |
A210S |
probably benign |
Het |
| Sh3bp1 |
A |
G |
15: 78,787,301 (GRCm39) |
K83E |
probably damaging |
Het |
| Sipa1l2 |
T |
C |
8: 126,166,012 (GRCm39) |
S1541G |
possibly damaging |
Het |
| Slc22a21 |
T |
C |
11: 53,870,673 (GRCm39) |
Y4C |
probably damaging |
Het |
| Smco1 |
C |
T |
16: 32,092,592 (GRCm39) |
H88Y |
probably damaging |
Het |
| Tll2 |
T |
C |
19: 41,084,336 (GRCm39) |
D697G |
probably damaging |
Het |
| Trim34a |
A |
G |
7: 103,910,200 (GRCm39) |
N334S |
possibly damaging |
Het |
| Ubqln1 |
A |
G |
13: 58,346,847 (GRCm39) |
I64T |
probably benign |
Het |
| Vstm2b |
T |
A |
7: 40,551,912 (GRCm39) |
|
probably null |
Het |
| Wdr17 |
A |
G |
8: 55,140,639 (GRCm39) |
F238L |
probably damaging |
Het |
| Wiz |
T |
C |
17: 32,596,822 (GRCm39) |
|
probably benign |
Het |
| Zfp407 |
T |
C |
18: 84,579,434 (GRCm39) |
S560G |
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 |
|
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 |
|
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'- TGTGCTGCTGATACACAGGC -3'
(R):5'- CAAGGGGCTATTACTAAAGAAATGC -3'
Sequencing Primer
(F):5'- TGCTGATACACAGGCTCCGTC -3'
(R):5'- GAAATGCATATTCTTGACACAACAC -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation