Incidental Mutation 'R7159:Pcdhga4'
| ID |
557542 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
045259-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.123)
|
| Stock # |
R7159 (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 37819972 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 507
(N507S)
|
| 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: N507S
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: N507S
| 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: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
99% (70/71) |
| 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: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Akap13 |
T |
A |
7: 75,380,327 (GRCm39) |
V500E |
possibly damaging |
Het |
| Ankrd34b |
T |
C |
13: 92,575,970 (GRCm39) |
S401P |
probably benign |
Het |
| Arfgef2 |
T |
A |
2: 166,668,848 (GRCm39) |
D41E |
probably benign |
Het |
| Arid1a |
T |
C |
4: 133,480,879 (GRCm39) |
N15S |
unknown |
Het |
| Arsa |
A |
T |
15: 89,358,921 (GRCm39) |
|
probably null |
Het |
| B3gnt9 |
C |
A |
8: 105,981,064 (GRCm39) |
C108F |
probably damaging |
Het |
| Bbc3 |
C |
A |
7: 16,047,733 (GRCm39) |
Y152* |
probably null |
Het |
| Btbd1 |
T |
C |
7: 81,467,957 (GRCm39) |
M188V |
probably benign |
Het |
| Caln1 |
C |
T |
5: 130,851,838 (GRCm39) |
T209I |
probably benign |
Het |
| Casp12 |
C |
T |
9: 5,353,763 (GRCm39) |
P266S |
possibly damaging |
Het |
| Ccm2l |
A |
T |
2: 152,912,787 (GRCm39) |
I109F |
probably damaging |
Het |
| Chst15 |
A |
C |
7: 131,871,987 (GRCm39) |
L98R |
probably damaging |
Het |
| Ctsq |
A |
G |
13: 61,186,737 (GRCm39) |
M89T |
probably benign |
Het |
| Ddx39b |
T |
C |
17: 35,465,986 (GRCm39) |
V169A |
probably benign |
Het |
| Fhad1 |
T |
C |
4: 141,678,927 (GRCm39) |
H583R |
probably benign |
Het |
| Fndc1 |
T |
A |
17: 8,019,763 (GRCm39) |
I139F |
probably damaging |
Het |
| Gm7145 |
C |
G |
1: 117,913,561 (GRCm39) |
H148D |
probably benign |
Het |
| Gpr62 |
C |
A |
9: 106,342,641 (GRCm39) |
A96S |
probably damaging |
Het |
| Gsap |
T |
A |
5: 21,475,618 (GRCm39) |
|
probably null |
Het |
| Hdhd5 |
T |
A |
6: 120,500,432 (GRCm39) |
T89S |
probably damaging |
Het |
| Kcna5 |
T |
A |
6: 126,510,592 (GRCm39) |
Y512F |
probably damaging |
Het |
| Krt84 |
C |
A |
15: 101,438,044 (GRCm39) |
E304* |
probably null |
Het |
| Krt9 |
TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC |
TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC |
11: 100,079,903 (GRCm39) |
|
probably benign |
Het |
| Lrp6 |
C |
A |
6: 134,484,514 (GRCm39) |
V370L |
probably benign |
Het |
| Lrrc3c |
G |
A |
11: 98,490,144 (GRCm39) |
G167D |
probably damaging |
Het |
| Man2b1 |
C |
T |
8: 85,813,909 (GRCm39) |
T291M |
probably benign |
Het |
| Mapkbp1 |
A |
G |
2: 119,855,613 (GRCm39) |
E1438G |
possibly damaging |
Het |
| Med12l |
A |
G |
3: 59,183,438 (GRCm39) |
T1947A |
probably benign |
Het |
| Myh15 |
A |
T |
16: 48,881,937 (GRCm39) |
T60S |
probably damaging |
Het |
| Myo5a |
A |
T |
9: 75,078,845 (GRCm39) |
I868F |
probably benign |
Het |
| Myom3 |
A |
T |
4: 135,536,162 (GRCm39) |
I1278F |
probably damaging |
Het |
| Nbn |
G |
T |
4: 15,983,677 (GRCm39) |
|
probably null |
Het |
| Ncam2 |
G |
T |
16: 81,287,262 (GRCm39) |
S392I |
probably damaging |
Het |
| Nrg3 |
A |
C |
14: 38,092,692 (GRCm39) |
L647* |
probably null |
Het |
| Or10j7 |
A |
T |
1: 173,011,890 (GRCm39) |
L37Q |
possibly damaging |
Het |
| Or2t35 |
T |
C |
14: 14,407,251 (GRCm38) |
S8P |
possibly damaging |
Het |
| Or2y1g |
A |
T |
11: 49,171,185 (GRCm39) |
D70V |
probably damaging |
Het |
| Or8j3c |
T |
A |
2: 86,253,956 (GRCm39) |
|
probably null |
Het |
| Pcdhb9 |
A |
G |
18: 37,534,545 (GRCm39) |
N180D |
possibly damaging |
Het |
| Pdilt |
A |
G |
7: 119,087,174 (GRCm39) |
V492A |
probably benign |
Het |
| Phf12 |
A |
G |
11: 77,914,366 (GRCm39) |
T603A |
possibly damaging |
Het |
| Phox2b |
T |
A |
5: 67,254,928 (GRCm39) |
I174F |
probably benign |
Het |
| Polq |
A |
T |
16: 36,883,215 (GRCm39) |
Q1793L |
possibly damaging |
Het |
| Prmt9 |
T |
C |
8: 78,282,393 (GRCm39) |
F97L |
probably benign |
Het |
| Prpsap1 |
T |
C |
11: 116,384,870 (GRCm39) |
E13G |
probably benign |
Het |
| Ptpru |
A |
G |
4: 131,546,851 (GRCm39) |
L280P |
probably damaging |
Het |
| Pygl |
A |
T |
12: 70,244,180 (GRCm39) |
M587K |
probably benign |
Het |
| Rc3h2 |
T |
C |
2: 37,299,659 (GRCm39) |
S124G |
probably benign |
Het |
| Rdh5 |
A |
G |
10: 128,754,184 (GRCm39) |
I83T |
possibly damaging |
Het |
| Rigi |
A |
G |
4: 40,213,804 (GRCm39) |
V618A |
probably benign |
Het |
| Ryr2 |
T |
G |
13: 11,825,794 (GRCm39) |
R561S |
probably damaging |
Het |
| Scara3 |
A |
G |
14: 66,158,229 (GRCm39) |
L593P |
probably damaging |
Het |
| Scfd2 |
T |
C |
5: 74,692,004 (GRCm39) |
I93V |
probably benign |
Het |
| Sema4f |
C |
A |
6: 82,894,864 (GRCm39) |
V444L |
possibly damaging |
Het |
| Slco1a7 |
T |
A |
6: 141,719,504 (GRCm39) |
M1L |
probably damaging |
Het |
| Spata33 |
T |
C |
8: 123,941,134 (GRCm39) |
L61P |
unknown |
Het |
| Stard10 |
A |
T |
7: 100,992,343 (GRCm39) |
|
probably null |
Het |
| Stub1 |
T |
C |
17: 26,051,038 (GRCm39) |
I115V |
probably benign |
Het |
| Tlcd3b |
T |
C |
7: 126,426,667 (GRCm39) |
F80S |
probably damaging |
Het |
| Tmem247 |
C |
T |
17: 87,225,710 (GRCm39) |
T50I |
probably benign |
Het |
| Tnrc6b |
A |
G |
15: 80,771,223 (GRCm39) |
M1103V |
possibly damaging |
Het |
| Trim61 |
T |
C |
8: 65,466,526 (GRCm39) |
Y245C |
probably benign |
Het |
| Trip13 |
T |
C |
13: 74,068,130 (GRCm39) |
I284V |
probably benign |
Het |
| Trpm4 |
T |
C |
7: 44,976,692 (GRCm39) |
|
probably null |
Het |
| Ttn |
C |
A |
2: 76,740,092 (GRCm39) |
L3528F |
unknown |
Het |
| Ttn |
A |
G |
2: 76,560,918 (GRCm39) |
L29161S |
probably damaging |
Het |
| Ube2v2 |
G |
A |
16: 15,398,948 (GRCm39) |
T47I |
probably benign |
Het |
| Vwa5b1 |
C |
T |
4: 138,302,733 (GRCm39) |
A921T |
possibly damaging |
Het |
| Xylt1 |
T |
A |
7: 117,236,829 (GRCm39) |
F526Y |
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 |
|
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'- GGTAGATATTAATGACAACCCGCC -3'
(R):5'- TGTCAGCTCCACACCAGTAG -3'
Sequencing Primer
(F):5'- GCCGACCTTCACCCATG -3'
(R):5'- CATCAGTGGGGATGGTGGGATAC -3'
|
| Posted On |
2019-06-26 |
Incidental Mutation