Incidental Mutation 'R9417:Pcdhga4'
| ID |
712142 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.123)
|
| Stock # |
R9417 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 37820560 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Serine
at position 703
(F703S)
|
| 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: F703S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: F703S
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.9%
- 20x: 99.6%
|
| Validation Efficiency |
|
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930553M12Rik |
A |
G |
4: 88,786,202 (GRCm39) |
Y139H |
unknown |
Het |
| Akr1b10 |
T |
C |
6: 34,371,027 (GRCm39) |
V259A |
probably benign |
Het |
| Aldh5a1 |
A |
T |
13: 25,095,673 (GRCm39) |
N481K |
probably damaging |
Het |
| Ankrd26 |
A |
T |
6: 118,504,725 (GRCm39) |
M728K |
possibly damaging |
Het |
| Asic1 |
A |
G |
15: 99,590,405 (GRCm39) |
M52V |
probably benign |
Het |
| Bean1 |
CT |
C |
8: 104,908,664 (GRCm39) |
|
probably null |
Het |
| Cacna2d2 |
C |
A |
9: 107,392,689 (GRCm39) |
Y544* |
probably null |
Het |
| Cdcp3 |
A |
G |
7: 130,852,218 (GRCm39) |
D818G |
possibly damaging |
Het |
| Chd4 |
A |
G |
6: 125,097,688 (GRCm39) |
N1403S |
probably damaging |
Het |
| Cldn4 |
G |
T |
5: 134,975,174 (GRCm39) |
N142K |
probably benign |
Het |
| Cracd |
GCGCGAGGCCGAGAGGCAGGAGGAGGAAGCAAGACAACGCGAGGCCGAGAGGCAGG |
GCGCGAGGCCGAGAGGCAGG |
5: 77,004,801 (GRCm39) |
|
probably benign |
Het |
| Dll1 |
T |
C |
17: 15,593,710 (GRCm39) |
Y219C |
probably damaging |
Het |
| Dnah2 |
T |
A |
11: 69,326,990 (GRCm39) |
I3539F |
probably damaging |
Het |
| Egfr |
T |
A |
11: 16,825,067 (GRCm39) |
L469* |
probably null |
Het |
| Elmo1 |
A |
G |
13: 20,756,573 (GRCm39) |
N554D |
possibly damaging |
Het |
| Fam234a |
A |
C |
17: 26,435,225 (GRCm39) |
F306L |
probably benign |
Het |
| Fbl |
G |
A |
7: 27,874,052 (GRCm39) |
G45D |
unknown |
Het |
| Fbxw10 |
C |
A |
11: 62,753,522 (GRCm39) |
C505* |
probably null |
Het |
| Ftcd |
G |
A |
10: 76,417,153 (GRCm39) |
G221S |
probably damaging |
Het |
| Gad1 |
A |
G |
2: 70,417,716 (GRCm39) |
D305G |
possibly damaging |
Het |
| Gdpd4 |
A |
G |
7: 97,607,074 (GRCm39) |
D16G |
probably benign |
Het |
| Gsdmc3 |
T |
A |
15: 63,738,663 (GRCm39) |
D133V |
possibly damaging |
Het |
| Hpdl |
T |
C |
4: 116,677,817 (GRCm39) |
T215A |
possibly damaging |
Het |
| Ift56 |
T |
C |
6: 38,386,386 (GRCm39) |
F369S |
probably damaging |
Het |
| Igsf10 |
A |
T |
3: 59,236,526 (GRCm39) |
N1218K |
possibly damaging |
Het |
| Isg20 |
C |
T |
7: 78,569,605 (GRCm39) |
P192L |
probably benign |
Het |
| Itga7 |
C |
T |
10: 128,793,543 (GRCm39) |
T126M |
unknown |
Het |
| Krr1 |
A |
G |
10: 111,813,026 (GRCm39) |
I134V |
probably benign |
Het |
| Krt71 |
T |
A |
15: 101,646,731 (GRCm39) |
T326S |
probably benign |
Het |
| Lamb1 |
T |
A |
12: 31,337,983 (GRCm39) |
V480E |
probably damaging |
Het |
| Mmp19 |
T |
A |
10: 128,630,523 (GRCm39) |
L102Q |
possibly damaging |
Het |
| Mtor |
T |
A |
4: 148,622,776 (GRCm39) |
L1952* |
probably null |
Het |
| Myo15a |
T |
A |
11: 60,378,243 (GRCm39) |
V215E |
|
Het |
| Nfs1 |
T |
A |
2: 155,965,851 (GRCm39) |
K77* |
probably null |
Het |
| Or52s1 |
A |
T |
7: 102,861,156 (GRCm39) |
I30F |
possibly damaging |
Het |
| Or9a4 |
T |
A |
6: 40,549,096 (GRCm39) |
Y259N |
|
Het |
| Pdzd7 |
A |
G |
19: 45,034,022 (GRCm39) |
S21P |
probably damaging |
Het |
| Pitrm1 |
A |
T |
13: 6,617,394 (GRCm39) |
I583F |
possibly damaging |
Het |
| Ppox |
A |
G |
1: 171,107,855 (GRCm39) |
L77P |
unknown |
Het |
| Ppp1r37 |
G |
T |
7: 19,269,658 (GRCm39) |
R114S |
probably damaging |
Het |
| Ppp4r3b |
T |
C |
11: 29,144,598 (GRCm39) |
V316A |
probably benign |
Het |
| Ptprd |
A |
G |
4: 75,865,335 (GRCm39) |
I1214T |
probably damaging |
Het |
| Rasal3 |
A |
G |
17: 32,615,441 (GRCm39) |
F466L |
probably benign |
Het |
| Ric8b |
A |
T |
10: 84,761,447 (GRCm39) |
D41V |
probably benign |
Het |
| Rin2 |
T |
C |
2: 145,686,713 (GRCm39) |
S81P |
probably benign |
Het |
| Sft2d1 |
T |
A |
17: 8,542,139 (GRCm39) |
C128S |
probably damaging |
Het |
| Skint1 |
T |
C |
4: 111,878,509 (GRCm39) |
V147A |
probably benign |
Het |
| Slc9c1 |
T |
C |
16: 45,413,848 (GRCm39) |
V992A |
probably benign |
Het |
| Sst |
A |
G |
16: 23,708,487 (GRCm39) |
S115P |
probably damaging |
Het |
| Sv2b |
G |
T |
7: 74,769,772 (GRCm39) |
S590Y |
probably damaging |
Het |
| Syne1 |
C |
T |
10: 5,082,021 (GRCm39) |
V868I |
probably benign |
Het |
| Tex35 |
T |
C |
1: 156,934,789 (GRCm39) |
I42V |
possibly damaging |
Het |
| Tlr2 |
T |
C |
3: 83,744,892 (GRCm39) |
N397S |
probably damaging |
Het |
| Tmem202 |
A |
G |
9: 59,431,999 (GRCm39) |
|
probably null |
Het |
| Usp20 |
A |
G |
2: 30,873,030 (GRCm39) |
|
probably null |
Het |
| Usp32 |
C |
T |
11: 84,885,369 (GRCm39) |
R1226Q |
probably damaging |
Het |
| Usp47 |
C |
T |
7: 111,688,801 (GRCm39) |
A736V |
possibly damaging |
Het |
| Vmn2r-ps117 |
T |
A |
17: 19,044,037 (GRCm39) |
L371* |
probably null |
Het |
| Wwp1 |
T |
A |
4: 19,662,215 (GRCm39) |
N127Y |
possibly damaging |
Het |
| Yae1d1 |
A |
T |
13: 18,167,770 (GRCm39) |
V41D |
probably damaging |
Het |
| Zbtb8b |
T |
C |
4: 129,326,517 (GRCm39) |
D216G |
probably benign |
Het |
| Zfp462 |
T |
C |
4: 55,016,988 (GRCm39) |
S903P |
probably benign |
Het |
| Zranb1 |
G |
A |
7: 132,585,466 (GRCm39) |
G638D |
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 |
|
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 |
|
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'- TGCTGGACAGAGATGCTCTC -3'
(R):5'- AGGATCACTCTTCCCACAGC -3'
Sequencing Primer
(F):5'- TCTCAAGCAGAGCCTGGTG -3'
(R):5'- GAAGATCAGGTGACTCTTCCCAG -3'
|
| Posted On |
2022-05-16 |
Incidental Mutation