Incidental Mutation 'R6208:Pcdhga4'
| ID |
503295 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
044342-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.123)
|
| Stock # |
R6208 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 37819762 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 437
(I437N)
|
| 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 |
probably damaging
Transcript: ENSMUST00000194418
AA Change: I437N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: I437N
| 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: ENSMUST00000195163
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000195624
|
| Meta Mutation Damage Score |
0.2036 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.7%
|
| Validation Efficiency |
98% (57/58) |
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Actl6a |
A |
T |
3: 32,766,043 (GRCm39) |
I18F |
probably benign |
Het |
| Apol11a |
C |
T |
15: 77,401,241 (GRCm39) |
R243C |
probably damaging |
Het |
| Asap3 |
A |
G |
4: 135,968,508 (GRCm39) |
M687V |
probably benign |
Het |
| Axdnd1 |
C |
T |
1: 156,220,426 (GRCm39) |
|
probably benign |
Het |
| Baz2b |
A |
G |
2: 59,755,150 (GRCm39) |
F1026S |
probably damaging |
Het |
| Bsg |
T |
C |
10: 79,544,672 (GRCm39) |
L70P |
probably damaging |
Het |
| Col10a1 |
A |
G |
10: 34,270,582 (GRCm39) |
N185D |
possibly damaging |
Het |
| Col6a2 |
T |
A |
10: 76,450,891 (GRCm39) |
N50I |
possibly damaging |
Het |
| Cux2 |
G |
A |
5: 121,998,885 (GRCm39) |
P1352S |
possibly damaging |
Het |
| Defa25 |
A |
G |
8: 21,575,197 (GRCm39) |
|
probably null |
Het |
| Emc1 |
G |
T |
4: 139,081,582 (GRCm39) |
R70L |
probably damaging |
Het |
| Fat1 |
T |
C |
8: 45,480,650 (GRCm39) |
F3028S |
probably damaging |
Het |
| Fhit |
T |
C |
14: 9,573,435 (GRCm38) |
E205G |
probably benign |
Het |
| Gaa |
C |
A |
11: 119,171,997 (GRCm39) |
A700D |
probably benign |
Het |
| Gm20830 |
T |
G |
Y: 6,916,792 (GRCm39) |
E109A |
probably benign |
Homo |
| Grm1 |
A |
T |
10: 10,595,690 (GRCm39) |
F646Y |
probably damaging |
Het |
| Hp1bp3 |
A |
G |
4: 137,944,481 (GRCm39) |
|
probably benign |
Het |
| Lce1d |
G |
A |
3: 92,593,312 (GRCm39) |
P34S |
unknown |
Het |
| Lpar1 |
G |
A |
4: 58,504,630 (GRCm39) |
Q13* |
probably null |
Het |
| Lrrc61 |
C |
T |
6: 48,545,839 (GRCm39) |
R221* |
probably null |
Het |
| Map2 |
A |
G |
1: 66,470,749 (GRCm39) |
N328D |
probably damaging |
Het |
| Mndal |
T |
A |
1: 173,684,988 (GRCm39) |
D527V |
possibly damaging |
Het |
| Mycbp2 |
T |
G |
14: 103,532,664 (GRCm39) |
N430T |
probably benign |
Het |
| Myo1e |
A |
G |
9: 70,283,887 (GRCm39) |
Y861C |
probably damaging |
Het |
| Nav2 |
A |
G |
7: 49,213,851 (GRCm39) |
T1622A |
probably damaging |
Het |
| Nom1 |
A |
T |
5: 29,654,617 (GRCm39) |
H773L |
possibly damaging |
Het |
| Npc2 |
G |
T |
12: 84,803,919 (GRCm39) |
P144Q |
probably damaging |
Het |
| Npnt |
A |
G |
3: 132,655,774 (GRCm39) |
|
probably benign |
Het |
| Nxpe4 |
A |
T |
9: 48,304,678 (GRCm39) |
Y255F |
probably benign |
Het |
| Obscn |
G |
A |
11: 58,958,474 (GRCm39) |
A3769V |
possibly damaging |
Het |
| Optc |
T |
C |
1: 133,832,737 (GRCm39) |
D121G |
probably damaging |
Het |
| Pard6a |
T |
C |
8: 106,428,866 (GRCm39) |
F26L |
probably damaging |
Het |
| Phf12 |
G |
T |
11: 77,914,417 (GRCm39) |
V71F |
probably damaging |
Het |
| Phf21b |
T |
A |
15: 84,679,317 (GRCm39) |
S282C |
probably damaging |
Het |
| Pou5f1 |
T |
C |
17: 35,821,357 (GRCm39) |
F323S |
possibly damaging |
Het |
| Psmd5 |
A |
T |
2: 34,757,023 (GRCm39) |
I67N |
probably damaging |
Het |
| Pyroxd1 |
A |
G |
6: 142,303,182 (GRCm39) |
K273R |
probably benign |
Het |
| Rnd2 |
C |
T |
11: 101,359,825 (GRCm39) |
L57F |
probably damaging |
Het |
| Rpusd1 |
A |
T |
17: 25,949,352 (GRCm39) |
H174L |
probably damaging |
Het |
| Ryr2 |
T |
C |
13: 11,910,106 (GRCm39) |
K94R |
probably benign |
Het |
| Scn2b |
A |
G |
9: 45,029,328 (GRCm39) |
R3G |
probably benign |
Het |
| Sf3b2 |
A |
T |
19: 5,325,126 (GRCm39) |
M782K |
possibly damaging |
Het |
| Skint7 |
A |
G |
4: 111,842,073 (GRCm39) |
|
probably null |
Het |
| Slc43a1 |
A |
G |
2: 84,687,184 (GRCm39) |
I319V |
possibly damaging |
Het |
| Snupn |
T |
A |
9: 56,890,247 (GRCm39) |
M356K |
probably damaging |
Het |
| Spata31d1a |
C |
A |
13: 59,848,378 (GRCm39) |
R1250M |
probably damaging |
Het |
| Sprr2h |
T |
C |
3: 92,294,216 (GRCm39) |
V21A |
unknown |
Het |
| Srpra |
A |
G |
9: 35,127,291 (GRCm39) |
T614A |
possibly damaging |
Het |
| Stk36 |
A |
T |
1: 74,650,591 (GRCm39) |
Q327L |
probably benign |
Het |
| Syne3 |
A |
G |
12: 104,909,622 (GRCm39) |
I738T |
probably benign |
Het |
| Tcea3 |
A |
T |
4: 135,975,360 (GRCm39) |
M1L |
probably damaging |
Het |
| Tead2 |
G |
T |
7: 44,867,526 (GRCm39) |
R85L |
probably damaging |
Het |
| Thap7 |
T |
C |
16: 17,346,300 (GRCm39) |
N228D |
possibly damaging |
Het |
| Trip11 |
T |
A |
12: 101,865,154 (GRCm39) |
E173V |
probably damaging |
Het |
| Ttc38 |
T |
A |
15: 85,725,698 (GRCm39) |
M187K |
possibly damaging |
Het |
| Vmn1r193 |
T |
A |
13: 22,403,138 (GRCm39) |
T285S |
possibly damaging |
Het |
| Vmn2r106 |
T |
C |
17: 20,488,591 (GRCm39) |
T603A |
probably damaging |
Het |
| Vps39 |
A |
T |
2: 120,163,897 (GRCm39) |
M355K |
probably damaging |
Het |
| Wnt5b |
G |
T |
6: 119,423,473 (GRCm39) |
L51I |
probably damaging |
Het |
| Xxylt1 |
A |
G |
16: 30,826,626 (GRCm39) |
Y230H |
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 |
|
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'- AACGGCCTTGTCACTTGTTC -3'
(R):5'- ACCGGTATTGGAGTTTATGGAGAC -3'
Sequencing Primer
(F):5'- TGTCACTTGTTCTATTCCAGATAATC -3'
(R):5'- ACATAGGTGCCCCCTGGATAG -3'
|
| Posted On |
2018-02-27 |
Incidental Mutation