Incidental Mutation 'R6937:Pcdh1'
| ID |
540364 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdh1
|
| Ensembl Gene |
ENSMUSG00000051375 |
| Gene Name |
protocadherin 1 |
| Synonyms |
2010005A06Rik |
| MMRRC Submission |
045051-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.330)
|
| Stock # |
R6937 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
38318967-38345023 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 38336528 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 36
(T36A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000124732
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000057185]
[ENSMUST00000159405]
[ENSMUST00000160721]
[ENSMUST00000161701]
[ENSMUST00000193828]
[ENSMUST00000194312]
|
| AlphaFold |
Q8CFX3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000057185
AA Change: T36A
PolyPhen 2
Score 0.298 (Sensitivity: 0.91; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: T36A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
33 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
36 |
120 |
2e-8 |
PFAM |
|
CA
|
168 |
256 |
5.18e-18 |
SMART |
|
CA
|
280 |
363 |
5.68e-24 |
SMART |
|
CA
|
395 |
482 |
1.84e-23 |
SMART |
|
CA
|
506 |
588 |
2.99e-32 |
SMART |
|
CA
|
612 |
691 |
9.36e-25 |
SMART |
|
CA
|
717 |
798 |
9.9e-15 |
SMART |
|
transmembrane domain
|
830 |
852 |
N/A |
INTRINSIC |
|
low complexity region
|
876 |
903 |
N/A |
INTRINSIC |
|
low complexity region
|
951 |
964 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159405
AA Change: T36A
PolyPhen 2
Score 0.298 (Sensitivity: 0.91; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: T36A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
33 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
36 |
120 |
2e-8 |
PFAM |
|
CA
|
168 |
256 |
5.18e-18 |
SMART |
|
CA
|
280 |
363 |
5.68e-24 |
SMART |
|
CA
|
395 |
482 |
1.84e-23 |
SMART |
|
CA
|
506 |
588 |
2.99e-32 |
SMART |
|
CA
|
612 |
691 |
9.36e-25 |
SMART |
|
CA
|
717 |
798 |
9.9e-15 |
SMART |
|
transmembrane domain
|
830 |
852 |
N/A |
INTRINSIC |
|
low complexity region
|
876 |
903 |
N/A |
INTRINSIC |
|
low complexity region
|
951 |
964 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000160721
AA Change: T36A
PolyPhen 2
Score 0.863 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375
AA Change: T36A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
33 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
36 |
120 |
9.9e-10 |
PFAM |
|
CA
|
168 |
256 |
5.18e-18 |
SMART |
|
low complexity region
|
310 |
321 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161701
|
| SMART Domains |
Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
29 |
117 |
5.18e-18 |
SMART |
|
CA
|
141 |
224 |
5.68e-24 |
SMART |
|
CA
|
256 |
343 |
1.84e-23 |
SMART |
|
CA
|
367 |
449 |
2.99e-32 |
SMART |
|
CA
|
473 |
552 |
9.36e-25 |
SMART |
|
CA
|
578 |
659 |
9.9e-15 |
SMART |
|
transmembrane domain
|
691 |
713 |
N/A |
INTRINSIC |
|
low complexity region
|
737 |
764 |
N/A |
INTRINSIC |
|
low complexity region
|
812 |
825 |
N/A |
INTRINSIC |
|
low complexity region
|
903 |
914 |
N/A |
INTRINSIC |
|
low complexity region
|
1029 |
1040 |
N/A |
INTRINSIC |
|
low complexity region
|
1059 |
1071 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000193828
AA Change: T51A
|
| SMART Domains |
Protein: ENSMUSP00000142328
Gene: ENSMUSG00000051375
AA Change: T51A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
18 |
48 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000194312
AA Change: T36A
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.1%
- 20x: 97.1%
|
| Validation Efficiency |
98% (42/43) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ankrd52 |
T |
C |
10: 128,222,889 (GRCm39) |
V613A |
probably benign |
Het |
| Cdh23 |
A |
T |
10: 60,322,893 (GRCm39) |
L337Q |
probably damaging |
Het |
| Chrna6 |
A |
G |
8: 27,897,055 (GRCm39) |
L274P |
probably damaging |
Het |
| Ciita |
G |
A |
16: 10,330,355 (GRCm39) |
|
probably null |
Het |
| Csnka2ip |
A |
T |
16: 64,299,058 (GRCm39) |
|
probably benign |
Het |
| Ddx60 |
G |
A |
8: 62,490,103 (GRCm39) |
D1691N |
probably damaging |
Het |
| Dnah7b |
T |
C |
1: 46,234,280 (GRCm39) |
I1441T |
probably damaging |
Het |
| Dock4 |
T |
C |
12: 40,884,634 (GRCm39) |
S1713P |
probably benign |
Het |
| Ep400 |
T |
C |
5: 110,859,018 (GRCm39) |
|
probably benign |
Het |
| Epn1 |
T |
C |
7: 5,092,943 (GRCm39) |
I85T |
probably damaging |
Het |
| Eri2 |
T |
C |
7: 119,386,012 (GRCm39) |
K228E |
probably damaging |
Het |
| Garem1 |
C |
T |
18: 21,280,827 (GRCm39) |
A510T |
probably benign |
Het |
| Gfm2 |
T |
A |
13: 97,299,572 (GRCm39) |
|
probably null |
Het |
| Hnrnpd |
T |
C |
5: 100,111,629 (GRCm39) |
T321A |
probably benign |
Het |
| Htr2a |
A |
T |
14: 74,882,604 (GRCm39) |
I197F |
probably damaging |
Het |
| Krtap2-4 |
T |
A |
11: 99,505,299 (GRCm39) |
|
probably benign |
Het |
| Lcn3 |
C |
A |
2: 25,657,823 (GRCm39) |
Y179* |
probably null |
Het |
| Mak |
A |
T |
13: 41,201,578 (GRCm39) |
M261K |
probably damaging |
Het |
| Marchf7 |
A |
G |
2: 60,071,310 (GRCm39) |
T605A |
probably damaging |
Het |
| Mcm4 |
A |
C |
16: 15,454,199 (GRCm39) |
F83V |
probably benign |
Het |
| Myo18b |
T |
C |
5: 112,950,258 (GRCm39) |
N1546S |
probably benign |
Het |
| Nckap1 |
T |
A |
2: 80,339,060 (GRCm39) |
K989N |
probably damaging |
Het |
| Ndufaf5 |
A |
G |
2: 140,023,522 (GRCm39) |
D119G |
probably damaging |
Het |
| Or7g28 |
A |
T |
9: 19,271,985 (GRCm39) |
V222D |
probably damaging |
Het |
| Pitpna |
C |
T |
11: 75,494,557 (GRCm39) |
T100I |
possibly damaging |
Het |
| Pmf1 |
A |
T |
3: 88,306,496 (GRCm39) |
L102Q |
probably damaging |
Het |
| Rftn2 |
T |
C |
1: 55,233,508 (GRCm39) |
|
probably null |
Het |
| Robo3 |
A |
G |
9: 37,341,176 (GRCm39) |
L10P |
probably benign |
Het |
| Serpinb6a |
T |
C |
13: 34,102,801 (GRCm39) |
I241V |
possibly damaging |
Het |
| St14 |
A |
T |
9: 31,040,956 (GRCm39) |
|
probably null |
Het |
| Stat6 |
T |
C |
10: 127,494,571 (GRCm39) |
|
probably null |
Het |
| Tdpoz6 |
T |
C |
3: 93,599,523 (GRCm39) |
N282S |
probably benign |
Het |
| Tdpoz8 |
A |
G |
3: 92,981,417 (GRCm39) |
H145R |
probably benign |
Het |
| Tenm4 |
G |
A |
7: 96,202,703 (GRCm39) |
R106H |
probably benign |
Het |
| Tgfbrap1 |
A |
T |
1: 43,091,064 (GRCm39) |
V687E |
probably damaging |
Het |
| Trim30d |
A |
T |
7: 104,132,634 (GRCm39) |
S68T |
probably damaging |
Het |
| Ttn |
A |
G |
2: 76,663,253 (GRCm39) |
|
probably benign |
Het |
| Ugt3a1 |
A |
T |
15: 9,292,158 (GRCm39) |
D97V |
probably benign |
Het |
| Ugt8a |
G |
A |
3: 125,709,250 (GRCm39) |
|
probably benign |
Het |
| Vmn1r184 |
A |
T |
7: 25,966,750 (GRCm39) |
K165N |
probably benign |
Het |
| Vmn2r86 |
T |
A |
10: 130,284,523 (GRCm39) |
I523F |
probably damaging |
Het |
| Wapl |
G |
A |
14: 34,444,311 (GRCm39) |
V588I |
probably benign |
Het |
| Wdr7 |
C |
T |
18: 63,924,938 (GRCm39) |
P974S |
probably benign |
Het |
| Zfp975 |
T |
C |
7: 42,314,480 (GRCm39) |
D31G |
possibly damaging |
Het |
|
| Other mutations in Pcdh1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00714:Pcdh1
|
APN |
18 |
38,331,782 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
IGL00919:Pcdh1
|
APN |
18 |
38,335,865 (GRCm39) |
nonsense |
probably null |
|
|
IGL01744:Pcdh1
|
APN |
18 |
38,336,302 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4260001:Pcdh1
|
UTSW |
18 |
38,336,419 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0542:Pcdh1
|
UTSW |
18 |
38,322,975 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1449:Pcdh1
|
UTSW |
18 |
38,322,929 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1540:Pcdh1
|
UTSW |
18 |
38,322,779 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1642:Pcdh1
|
UTSW |
18 |
38,332,283 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R1672:Pcdh1
|
UTSW |
18 |
38,325,233 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1695:Pcdh1
|
UTSW |
18 |
38,335,921 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1727:Pcdh1
|
UTSW |
18 |
38,336,085 (GRCm39) |
nonsense |
probably null |
|
|
R1781:Pcdh1
|
UTSW |
18 |
38,322,977 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1793:Pcdh1
|
UTSW |
18 |
38,331,938 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1839:Pcdh1
|
UTSW |
18 |
38,332,538 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R1843:Pcdh1
|
UTSW |
18 |
38,325,278 (GRCm39) |
splice site |
probably null |
|
|
R1882:Pcdh1
|
UTSW |
18 |
38,335,895 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R2261:Pcdh1
|
UTSW |
18 |
38,331,710 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2262:Pcdh1
|
UTSW |
18 |
38,331,710 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2263:Pcdh1
|
UTSW |
18 |
38,331,710 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2511:Pcdh1
|
UTSW |
18 |
38,332,532 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R2937:Pcdh1
|
UTSW |
18 |
38,322,815 (GRCm39) |
missense |
probably benign |
0.40 |
|
R3941:Pcdh1
|
UTSW |
18 |
38,332,511 (GRCm39) |
missense |
probably benign |
0.02 |
|
R3942:Pcdh1
|
UTSW |
18 |
38,332,511 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4057:Pcdh1
|
UTSW |
18 |
38,331,950 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4155:Pcdh1
|
UTSW |
18 |
38,336,159 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4169:Pcdh1
|
UTSW |
18 |
38,331,358 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4617:Pcdh1
|
UTSW |
18 |
38,330,913 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4690:Pcdh1
|
UTSW |
18 |
38,336,528 (GRCm39) |
missense |
probably benign |
0.33 |
|
R4825:Pcdh1
|
UTSW |
18 |
38,322,912 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R5201:Pcdh1
|
UTSW |
18 |
38,331,971 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5266:Pcdh1
|
UTSW |
18 |
38,325,252 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5267:Pcdh1
|
UTSW |
18 |
38,325,252 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5351:Pcdh1
|
UTSW |
18 |
38,330,819 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5568:Pcdh1
|
UTSW |
18 |
38,330,420 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5729:Pcdh1
|
UTSW |
18 |
38,335,999 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5731:Pcdh1
|
UTSW |
18 |
38,331,651 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6043:Pcdh1
|
UTSW |
18 |
38,336,327 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R6278:Pcdh1
|
UTSW |
18 |
38,332,263 (GRCm39) |
missense |
probably benign |
0.29 |
|
R6333:Pcdh1
|
UTSW |
18 |
38,331,860 (GRCm39) |
missense |
probably benign |
0.25 |
|
R6498:Pcdh1
|
UTSW |
18 |
38,330,490 (GRCm39) |
missense |
probably benign |
0.18 |
|
R6994:Pcdh1
|
UTSW |
18 |
38,331,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7242:Pcdh1
|
UTSW |
18 |
38,336,270 (GRCm39) |
missense |
probably benign |
0.06 |
|
R7289:Pcdh1
|
UTSW |
18 |
38,322,966 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7391:Pcdh1
|
UTSW |
18 |
38,335,838 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7702:Pcdh1
|
UTSW |
18 |
38,336,569 (GRCm39) |
missense |
unknown |
|
|
R7738:Pcdh1
|
UTSW |
18 |
38,330,529 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7849:Pcdh1
|
UTSW |
18 |
38,322,662 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7941:Pcdh1
|
UTSW |
18 |
38,332,133 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8109:Pcdh1
|
UTSW |
18 |
38,332,049 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8675:Pcdh1
|
UTSW |
18 |
38,332,229 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8851:Pcdh1
|
UTSW |
18 |
38,325,155 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8947:Pcdh1
|
UTSW |
18 |
38,332,073 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R9443:Pcdh1
|
UTSW |
18 |
38,330,633 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9448:Pcdh1
|
UTSW |
18 |
38,330,492 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9608:Pcdh1
|
UTSW |
18 |
38,330,904 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
X0027:Pcdh1
|
UTSW |
18 |
38,322,841 (GRCm39) |
nonsense |
probably null |
|
|
Z1088:Pcdh1
|
UTSW |
18 |
38,331,120 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Pcdh1
|
UTSW |
18 |
38,331,741 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCTGGTTCTGGCATTCACG -3'
(R):5'- ACAGCCTTCCGAGTCAGTTTC -3'
Sequencing Primer
(F):5'- CCTCTCGATCAATGGAGGTC -3'
(R):5'- AGTCAGTTTCTTCTCCATAGCTGATG -3'
|
| Posted On |
2018-11-06 |
Incidental Mutation