Incidental Mutation 'R5186:Pcdhga4'
| ID |
397926 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
042765-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.132)
|
| Stock # |
R5186 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 37820479 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Isoleucine
at position 676
(N676I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000142140
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000073447]
[ENSMUST00000115661]
[ENSMUST00000192931]
[ENSMUST00000193869]
[ENSMUST00000194190]
[ENSMUST00000194418]
[ENSMUST00000195112]
[ENSMUST00000194544]
|
| 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: N181I
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194418
AA Change: N676I
PolyPhen 2
Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: N676I
| 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: 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: ENSMUST00000194544
|
| SMART Domains |
Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:CA
|
18 |
66 |
5e-20 |
BLAST |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 95.0%
|
| 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: 72 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8a |
T |
C |
11: 109,982,425 (GRCm39) |
I6V |
probably null |
Het |
| Aox1 |
A |
G |
1: 58,107,529 (GRCm39) |
D601G |
probably damaging |
Het |
| Asic1 |
GCACC |
GCACCACC |
15: 99,596,684 (GRCm39) |
|
probably benign |
Het |
| Cacna1g |
T |
G |
11: 94,333,674 (GRCm39) |
N931T |
probably damaging |
Het |
| Ccdc14 |
T |
C |
16: 34,541,955 (GRCm39) |
F511L |
probably damaging |
Het |
| Cd177 |
T |
A |
7: 24,444,348 (GRCm39) |
E710V |
probably benign |
Het |
| Cep112 |
T |
C |
11: 108,643,386 (GRCm39) |
C49R |
probably benign |
Het |
| Clip2 |
G |
A |
5: 134,551,645 (GRCm39) |
T159M |
possibly damaging |
Het |
| Dnah2 |
T |
C |
11: 69,326,710 (GRCm39) |
N3575S |
probably damaging |
Het |
| Dnah6 |
T |
A |
6: 73,044,410 (GRCm39) |
I3234F |
probably damaging |
Het |
| Eci3 |
G |
T |
13: 35,130,961 (GRCm39) |
A302E |
possibly damaging |
Het |
| Fam204a |
T |
C |
19: 60,188,421 (GRCm39) |
K214E |
probably damaging |
Het |
| Fam78a |
T |
C |
2: 31,972,666 (GRCm39) |
T85A |
possibly damaging |
Het |
| Flnb |
T |
C |
14: 7,909,748 (GRCm38) |
Y1401H |
probably damaging |
Het |
| Foxl2 |
A |
T |
9: 98,838,108 (GRCm39) |
D132V |
probably damaging |
Het |
| Frs2 |
C |
A |
10: 116,914,747 (GRCm39) |
W57C |
probably damaging |
Het |
| Gm26558 |
G |
T |
2: 70,491,761 (GRCm39) |
|
probably benign |
Het |
| Gpr139 |
A |
G |
7: 118,744,063 (GRCm39) |
V174A |
probably benign |
Het |
| Grik5 |
T |
C |
7: 24,715,244 (GRCm39) |
T676A |
probably damaging |
Het |
| H60c |
T |
C |
10: 3,209,273 (GRCm39) |
|
probably null |
Het |
| Hspa1l |
A |
G |
17: 35,197,445 (GRCm39) |
K495E |
probably damaging |
Het |
| Irgm1 |
C |
T |
11: 48,757,044 (GRCm39) |
V256I |
probably benign |
Het |
| Kat7 |
T |
A |
11: 95,177,242 (GRCm39) |
T293S |
probably benign |
Het |
| Lipg |
C |
T |
18: 75,094,009 (GRCm39) |
V13I |
probably benign |
Het |
| Lrrn1 |
A |
T |
6: 107,546,185 (GRCm39) |
Y661F |
probably damaging |
Het |
| Mllt3 |
A |
G |
4: 87,759,232 (GRCm39) |
V272A |
probably benign |
Het |
| Mx1 |
G |
A |
16: 97,256,694 (GRCm39) |
R162C |
probably benign |
Het |
| Myo18b |
T |
A |
5: 113,019,336 (GRCm39) |
D647V |
probably damaging |
Het |
| Naf1 |
G |
A |
8: 67,332,298 (GRCm39) |
V329I |
probably benign |
Het |
| Or4k40 |
A |
T |
2: 111,251,119 (GRCm39) |
M59K |
probably damaging |
Het |
| Or52u1 |
A |
T |
7: 104,237,418 (GRCm39) |
I153F |
probably damaging |
Het |
| Or8g22 |
A |
T |
9: 38,958,265 (GRCm39) |
C194* |
probably null |
Het |
| P2rx5 |
G |
A |
11: 73,062,616 (GRCm39) |
V442M |
possibly damaging |
Het |
| Pcdhb9 |
A |
G |
18: 37,534,285 (GRCm39) |
E93G |
probably damaging |
Het |
| Pgm5 |
A |
G |
19: 24,797,492 (GRCm39) |
M230T |
probably damaging |
Het |
| Pik3c2g |
T |
C |
6: 139,599,016 (GRCm39) |
V44A |
probably damaging |
Het |
| Pp2d1 |
T |
C |
17: 53,815,168 (GRCm39) |
M519V |
probably benign |
Het |
| Ppp1r10 |
A |
G |
17: 36,239,403 (GRCm39) |
E404G |
probably damaging |
Het |
| Prpf8 |
A |
T |
11: 75,380,609 (GRCm39) |
E104V |
possibly damaging |
Het |
| Ptpra |
T |
C |
2: 30,328,367 (GRCm39) |
|
probably null |
Het |
| Pygl |
A |
C |
12: 70,248,118 (GRCm39) |
N248K |
probably damaging |
Het |
| Rbm8a |
A |
G |
3: 96,538,248 (GRCm39) |
D102G |
probably damaging |
Het |
| Sema3d |
A |
G |
5: 12,634,875 (GRCm39) |
D647G |
probably benign |
Het |
| Serpinb11 |
A |
T |
1: 107,307,484 (GRCm39) |
D305V |
probably damaging |
Het |
| Slc12a8 |
T |
C |
16: 33,437,578 (GRCm39) |
I337T |
probably damaging |
Het |
| Slc29a2 |
G |
A |
19: 5,078,995 (GRCm39) |
R286Q |
probably benign |
Het |
| Slc2a3 |
T |
A |
6: 122,712,542 (GRCm39) |
D234V |
probably damaging |
Het |
| Slco4a1 |
T |
C |
2: 180,114,901 (GRCm39) |
V608A |
probably damaging |
Het |
| Spata31d1e |
A |
T |
13: 59,891,553 (GRCm39) |
L89H |
probably damaging |
Het |
| Srrm2 |
C |
T |
17: 24,035,561 (GRCm39) |
T831I |
probably benign |
Het |
| St18 |
T |
A |
1: 6,872,541 (GRCm39) |
|
probably null |
Het |
| Tesk2 |
G |
C |
4: 116,599,093 (GRCm39) |
G67A |
probably damaging |
Het |
| Tlr1 |
A |
T |
5: 65,082,564 (GRCm39) |
L671H |
probably damaging |
Het |
| Tmem63b |
A |
T |
17: 45,972,403 (GRCm39) |
Y735N |
possibly damaging |
Het |
| Tmprss11a |
C |
T |
5: 86,567,938 (GRCm39) |
C263Y |
probably damaging |
Het |
| Trio |
A |
T |
15: 27,898,077 (GRCm39) |
V345E |
probably damaging |
Het |
| Tut7 |
A |
G |
13: 59,964,470 (GRCm39) |
|
probably null |
Het |
| Ubr5 |
A |
G |
15: 37,998,160 (GRCm39) |
S1674P |
probably damaging |
Het |
| Uchl3 |
T |
A |
14: 101,933,353 (GRCm39) |
C209S |
probably damaging |
Het |
| Uhmk1 |
T |
C |
1: 170,038,736 (GRCm39) |
N206S |
probably damaging |
Het |
| Uhrf1 |
C |
T |
17: 56,625,340 (GRCm39) |
R588W |
probably damaging |
Het |
| Usp28 |
T |
C |
9: 48,921,550 (GRCm39) |
V256A |
probably damaging |
Het |
| Utrn |
C |
A |
10: 12,604,521 (GRCm39) |
L552F |
probably damaging |
Het |
| Vmn1r55 |
A |
T |
7: 5,149,985 (GRCm39) |
M146K |
probably damaging |
Het |
| Vmn1r57 |
A |
C |
7: 5,224,107 (GRCm39) |
I211L |
probably benign |
Het |
| Zar1 |
C |
T |
5: 72,734,742 (GRCm39) |
C316Y |
probably damaging |
Het |
| Zc3h11a |
A |
T |
1: 133,549,412 (GRCm39) |
S750T |
probably damaging |
Het |
| Zfp366 |
G |
A |
13: 99,382,676 (GRCm39) |
C613Y |
probably benign |
Het |
| Zfp37 |
A |
T |
4: 62,109,493 (GRCm39) |
C524S |
probably damaging |
Het |
| Zfp516 |
T |
C |
18: 82,975,218 (GRCm39) |
V472A |
probably benign |
Het |
| Zhx1 |
A |
T |
15: 57,915,819 (GRCm39) |
M809K |
probably damaging |
Het |
| Zic1 |
T |
C |
9: 91,246,424 (GRCm39) |
Y216C |
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 |
|
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 |
|
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'- GGCCGTAGACAAAGACTCAG -3'
(R):5'- TGACAACCCATTACCTGCAG -3'
Sequencing Primer
(F):5'- AGAACGCCTGGCTGTCCTAC -3'
(R):5'- TTACCTGCAGCCTGAAGC -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation