Incidental Mutation 'R8109:Sycp1'
| ID |
643852 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp1
|
| Ensembl Gene |
ENSMUSG00000027855 |
| Gene Name |
synaptonemal complex protein 1 |
| Synonyms |
SCP1 |
| MMRRC Submission |
067538-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.539)
|
| Stock # |
R8109 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 102758918 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 780
(S780T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000029448
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000196988]
|
| AlphaFold |
Q62209 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029448
AA Change: S780T
PolyPhen 2
Score 0.206 (Sensitivity: 0.92; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: S780T
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000196988
AA Change: S780T
PolyPhen 2
Score 0.206 (Sensitivity: 0.92; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: S780T
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.5%
|
| Validation Efficiency |
98% (47/48) |
| MGI Phenotype |
PHENOTYPE: Homozygous null mice display male and female infertility, azoospermia, small ovary, small testis and seminiferous tubules, absent ovarian follicles, and failure of synapse formation during meiosis. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aars1 |
T |
C |
8: 111,767,284 (GRCm39) |
V130A |
probably benign |
Het |
| Acte1 |
C |
T |
7: 143,451,203 (GRCm39) |
|
probably null |
Het |
| Adamts12 |
A |
C |
15: 11,331,877 (GRCm39) |
K1465T |
probably benign |
Het |
| Adamtsl1 |
T |
C |
4: 86,166,306 (GRCm39) |
V223A |
|
Het |
| Adamtsl3 |
T |
A |
7: 82,251,487 (GRCm39) |
I1494N |
possibly damaging |
Het |
| Ank3 |
T |
C |
10: 69,826,148 (GRCm39) |
Y1606H |
|
Het |
| Arhgap32 |
A |
G |
9: 32,093,150 (GRCm39) |
I168V |
probably benign |
Het |
| Atxn7l2 |
G |
A |
3: 108,110,617 (GRCm39) |
R675C |
probably damaging |
Het |
| Brcc3dc |
A |
G |
10: 108,535,520 (GRCm39) |
M145T |
probably damaging |
Het |
| Bst2 |
A |
T |
8: 71,989,990 (GRCm39) |
W28R |
probably damaging |
Het |
| Cadps |
T |
A |
14: 12,488,975 (GRCm38) |
T861S |
probably benign |
Het |
| Ceacam11 |
A |
G |
7: 17,709,243 (GRCm39) |
Y147C |
probably benign |
Het |
| Clasp2 |
T |
A |
9: 113,740,588 (GRCm39) |
N1187K |
probably damaging |
Het |
| Dcaf7 |
T |
C |
11: 105,937,604 (GRCm39) |
W76R |
probably damaging |
Het |
| Ephb1 |
G |
A |
9: 101,918,222 (GRCm39) |
T429I |
probably damaging |
Het |
| Flg |
A |
T |
3: 93,197,734 (GRCm39) |
Q21L |
unknown |
Het |
| Flrt2 |
T |
C |
12: 95,747,333 (GRCm39) |
V557A |
probably benign |
Het |
| Gdpgp1 |
T |
C |
7: 79,888,581 (GRCm39) |
V204A |
probably damaging |
Het |
| Gmcl1 |
G |
T |
6: 86,698,408 (GRCm39) |
A163E |
probably damaging |
Het |
| Gpr137b |
T |
C |
13: 13,533,991 (GRCm39) |
Y355C |
|
Het |
| Jph2 |
T |
C |
2: 163,181,206 (GRCm39) |
K653E |
probably benign |
Het |
| Kmt2c |
T |
C |
5: 25,486,382 (GRCm39) |
S4724G |
probably damaging |
Het |
| Llgl2 |
T |
C |
11: 115,741,619 (GRCm39) |
V583A |
possibly damaging |
Het |
| Met |
T |
C |
6: 17,562,236 (GRCm39) |
V1199A |
probably damaging |
Het |
| Mmp25 |
A |
G |
17: 23,863,768 (GRCm39) |
W21R |
probably benign |
Het |
| Nsun4 |
A |
T |
4: 115,909,040 (GRCm39) |
C507S |
probably benign |
Het |
| Or1j19 |
T |
A |
2: 36,676,618 (GRCm39) |
M27K |
probably benign |
Het |
| Pard6g |
T |
C |
18: 80,160,658 (GRCm39) |
V257A |
possibly damaging |
Het |
| Pcdh1 |
A |
G |
18: 38,332,049 (GRCm39) |
V457A |
probably damaging |
Het |
| Pcnx1 |
C |
T |
12: 81,965,593 (GRCm39) |
R59* |
probably null |
Het |
| Pdzd2 |
G |
A |
15: 12,373,592 (GRCm39) |
S2181L |
probably benign |
Het |
| Plpp6 |
T |
A |
19: 28,941,891 (GRCm39) |
M164K |
possibly damaging |
Het |
| Rhobtb2 |
C |
A |
14: 70,038,080 (GRCm39) |
R60L |
probably damaging |
Het |
| Rsph10b |
A |
C |
5: 143,922,348 (GRCm39) |
I845L |
probably benign |
Het |
| Sdf4 |
C |
T |
4: 156,094,295 (GRCm39) |
A325V |
probably damaging |
Het |
| Slc4a3 |
A |
G |
1: 75,528,448 (GRCm39) |
D481G |
possibly damaging |
Het |
| Smo |
A |
G |
6: 29,755,522 (GRCm39) |
Y398C |
probably damaging |
Het |
| Sox18 |
A |
G |
2: 181,313,293 (GRCm39) |
Y8H |
possibly damaging |
Het |
| Tdg |
T |
A |
10: 82,480,353 (GRCm39) |
V239E |
probably damaging |
Het |
| Tenm2 |
T |
C |
11: 35,899,137 (GRCm39) |
T2675A |
probably benign |
Het |
| Thrap3 |
C |
A |
4: 126,080,273 (GRCm39) |
R31L |
unknown |
Het |
| Tinagl1 |
T |
A |
4: 130,063,123 (GRCm39) |
I149F |
probably damaging |
Het |
| Tnc |
A |
G |
4: 63,927,000 (GRCm39) |
V842A |
probably benign |
Het |
| Tpm3-rs7 |
A |
G |
14: 113,552,772 (GRCm39) |
D222G |
probably benign |
Het |
| Ube4a |
T |
C |
9: 44,846,781 (GRCm39) |
I773V |
probably benign |
Het |
| Vmn1r229 |
T |
C |
17: 21,035,268 (GRCm39) |
V171A |
probably benign |
Het |
| Zc3hav1 |
T |
C |
6: 38,306,114 (GRCm39) |
E646G |
probably damaging |
Het |
| Zfp341 |
A |
T |
2: 154,469,820 (GRCm39) |
M168L |
probably benign |
Het |
| Zfp874a |
A |
C |
13: 67,597,563 (GRCm39) |
D13E |
possibly damaging |
Het |
|
| Other mutations in Sycp1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00513:Sycp1
|
APN |
3 |
102,748,278 (GRCm39) |
missense |
probably benign |
|
|
IGL00833:Sycp1
|
APN |
3 |
102,783,617 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL01066:Sycp1
|
APN |
3 |
102,827,950 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01484:Sycp1
|
APN |
3 |
102,823,183 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL02139:Sycp1
|
APN |
3 |
102,772,430 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02270:Sycp1
|
APN |
3 |
102,803,259 (GRCm39) |
missense |
probably benign |
0.12 |
|
IGL02347:Sycp1
|
APN |
3 |
102,800,863 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02630:Sycp1
|
APN |
3 |
102,786,080 (GRCm39) |
splice site |
probably benign |
|
|
IGL02668:Sycp1
|
APN |
3 |
102,727,847 (GRCm39) |
splice site |
probably benign |
|
|
IGL02928:Sycp1
|
APN |
3 |
102,726,134 (GRCm39) |
utr 3 prime |
probably benign |
|
|
PIT4458001:Sycp1
|
UTSW |
3 |
102,842,149 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0027:Sycp1
|
UTSW |
3 |
102,803,226 (GRCm39) |
missense |
probably benign |
|
|
R0282:Sycp1
|
UTSW |
3 |
102,823,111 (GRCm39) |
splice site |
probably benign |
|
|
R0462:Sycp1
|
UTSW |
3 |
102,726,422 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R0609:Sycp1
|
UTSW |
3 |
102,806,165 (GRCm39) |
splice site |
probably null |
|
|
R0837:Sycp1
|
UTSW |
3 |
102,822,561 (GRCm39) |
missense |
probably benign |
0.17 |
|
R1301:Sycp1
|
UTSW |
3 |
102,827,938 (GRCm39) |
missense |
probably benign |
0.02 |
|
R2408:Sycp1
|
UTSW |
3 |
102,832,575 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2449:Sycp1
|
UTSW |
3 |
102,832,522 (GRCm39) |
missense |
probably benign |
0.15 |
|
R2516:Sycp1
|
UTSW |
3 |
102,752,382 (GRCm39) |
missense |
probably benign |
0.09 |
|
R2880:Sycp1
|
UTSW |
3 |
102,726,214 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R3410:Sycp1
|
UTSW |
3 |
102,748,357 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R3427:Sycp1
|
UTSW |
3 |
102,783,666 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4538:Sycp1
|
UTSW |
3 |
102,748,278 (GRCm39) |
missense |
probably benign |
|
|
R4679:Sycp1
|
UTSW |
3 |
102,829,778 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R4707:Sycp1
|
UTSW |
3 |
102,760,805 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R4785:Sycp1
|
UTSW |
3 |
102,760,805 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R5017:Sycp1
|
UTSW |
3 |
102,803,303 (GRCm39) |
splice site |
probably null |
|
|
R5036:Sycp1
|
UTSW |
3 |
102,727,916 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5044:Sycp1
|
UTSW |
3 |
102,752,370 (GRCm39) |
missense |
probably benign |
0.03 |
|
R5070:Sycp1
|
UTSW |
3 |
102,827,881 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5079:Sycp1
|
UTSW |
3 |
102,786,116 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R5289:Sycp1
|
UTSW |
3 |
102,841,569 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R5393:Sycp1
|
UTSW |
3 |
102,748,363 (GRCm39) |
splice site |
probably null |
|
|
R5477:Sycp1
|
UTSW |
3 |
102,726,206 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5576:Sycp1
|
UTSW |
3 |
102,726,218 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5814:Sycp1
|
UTSW |
3 |
102,803,213 (GRCm39) |
missense |
probably benign |
0.03 |
|
R6291:Sycp1
|
UTSW |
3 |
102,816,277 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6460:Sycp1
|
UTSW |
3 |
102,832,569 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6527:Sycp1
|
UTSW |
3 |
102,806,203 (GRCm39) |
missense |
probably benign |
0.09 |
|
R6870:Sycp1
|
UTSW |
3 |
102,842,919 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6873:Sycp1
|
UTSW |
3 |
102,748,296 (GRCm39) |
missense |
probably benign |
|
|
R7037:Sycp1
|
UTSW |
3 |
102,806,250 (GRCm39) |
missense |
possibly damaging |
0.62 |
|
R7210:Sycp1
|
UTSW |
3 |
102,760,808 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7405:Sycp1
|
UTSW |
3 |
102,832,543 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R7604:Sycp1
|
UTSW |
3 |
102,820,749 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7733:Sycp1
|
UTSW |
3 |
102,803,278 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7858:Sycp1
|
UTSW |
3 |
102,806,273 (GRCm39) |
missense |
probably benign |
0.09 |
|
R7909:Sycp1
|
UTSW |
3 |
102,727,942 (GRCm39) |
nonsense |
probably null |
|
|
R8141:Sycp1
|
UTSW |
3 |
102,842,885 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R8289:Sycp1
|
UTSW |
3 |
102,748,353 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8359:Sycp1
|
UTSW |
3 |
102,727,909 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8844:Sycp1
|
UTSW |
3 |
102,772,421 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9020:Sycp1
|
UTSW |
3 |
102,783,653 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9149:Sycp1
|
UTSW |
3 |
102,758,944 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GGGAAAGATAGTGAAAAGCTGTATTTT -3'
(R):5'- GCCTTGATGTTTAGGAGAGGAGA -3'
Sequencing Primer
(F):5'- GACATCAAGTTGAACCATAC -3'
(R):5'- ACTTACATTGAGTGAGGTTATGTTC -3'
|
| Posted On |
2020-09-02 |
Incidental Mutation