Incidental Mutation 'R8141:Sycp1'
ID |
632525 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Sycp1
|
Ensembl Gene |
ENSMUSG00000027855 |
Gene Name |
synaptonemal complex protein 1 |
Synonyms |
SCP1 |
MMRRC Submission |
067569-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.539)
|
Stock # |
R8141 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to T
at 102842885 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Alanine to Glutamic Acid
at position 28
(A28E)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000029448
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000058899]
[ENSMUST00000196988]
[ENSMUST00000199930]
|
AlphaFold |
Q62209 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000029448
AA Change: A28E
PolyPhen 2
Score 0.732 (Sensitivity: 0.86; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000029448 Gene: ENSMUSG00000027855 AA Change: A28E
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000058899
|
SMART Domains |
Protein: ENSMUSP00000052557 Gene: ENSMUSG00000048938
Domain | Start | End | E-Value | Type |
Blast:HOLI
|
2 |
47 |
5e-9 |
BLAST |
ZnF_C4
|
119 |
190 |
2.51e-36 |
SMART |
HOLI
|
289 |
474 |
1.74e-21 |
SMART |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000196988
AA Change: A28E
PolyPhen 2
Score 0.732 (Sensitivity: 0.86; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000143651 Gene: ENSMUSG00000027855 AA Change: A28E
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Predicted Effect |
unknown
Transcript: ENSMUST00000199930
AA Change: A28E
|
SMART Domains |
Protein: ENSMUSP00000143493 Gene: ENSMUSG00000027855 AA Change: A28E
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
95 |
2e-33 |
PFAM |
Pfam:SCP-1
|
93 |
182 |
9.8e-53 |
PFAM |
|
Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.6%
- 10x: 98.3%
- 20x: 90.7%
|
Validation Efficiency |
100% (59/59) |
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: 51 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700017B05Rik |
T |
C |
9: 57,165,688 (GRCm39) |
T229A |
probably benign |
Het |
4930438A08Rik |
A |
G |
11: 58,177,411 (GRCm39) |
E40G |
|
Het |
Actn2 |
T |
C |
13: 12,303,516 (GRCm39) |
D428G |
probably damaging |
Het |
Arl14epl |
C |
A |
18: 47,059,410 (GRCm39) |
N8K |
probably benign |
Het |
Bend7 |
T |
C |
2: 4,757,636 (GRCm39) |
V226A |
probably benign |
Het |
C1s1 |
A |
T |
6: 124,508,321 (GRCm39) |
L556Q |
probably damaging |
Het |
Casr |
T |
C |
16: 36,315,173 (GRCm39) |
K966E |
probably damaging |
Het |
Ccm2l |
T |
C |
2: 152,912,791 (GRCm39) |
L110P |
probably damaging |
Het |
Cdhr4 |
G |
A |
9: 107,873,991 (GRCm39) |
R59H |
|
Het |
Celf3 |
C |
A |
3: 94,395,850 (GRCm39) |
N410K |
probably damaging |
Het |
Cfap251 |
T |
G |
5: 123,424,493 (GRCm39) |
V726G |
possibly damaging |
Het |
Cpne6 |
T |
C |
14: 55,750,066 (GRCm39) |
C66R |
possibly damaging |
Het |
Cyp2f2 |
G |
A |
7: 26,828,678 (GRCm39) |
V183I |
probably benign |
Het |
Eln |
CTCCAGCTCCGAT |
C |
5: 134,758,003 (GRCm39) |
|
probably benign |
Het |
Fam53b |
A |
C |
7: 132,361,758 (GRCm39) |
V90G |
probably damaging |
Het |
Fat3 |
T |
A |
9: 15,908,362 (GRCm39) |
I2547F |
possibly damaging |
Het |
Foxk1 |
A |
G |
5: 142,439,716 (GRCm39) |
Y524C |
probably damaging |
Het |
Gpr87 |
A |
G |
3: 59,087,020 (GRCm39) |
S162P |
probably damaging |
Het |
Ifi204 |
A |
G |
1: 173,583,189 (GRCm39) |
V343A |
possibly damaging |
Het |
Igsf10 |
A |
G |
3: 59,237,949 (GRCm39) |
L744P |
probably damaging |
Het |
Iqub |
T |
A |
6: 24,491,608 (GRCm39) |
K359N |
probably benign |
Het |
Kdm3b |
A |
T |
18: 34,961,599 (GRCm39) |
K1459* |
probably null |
Het |
Kirrel1 |
C |
T |
3: 86,993,735 (GRCm39) |
W507* |
probably null |
Het |
Klra17 |
T |
C |
6: 129,849,292 (GRCm39) |
D94G |
probably damaging |
Het |
Llgl1 |
G |
C |
11: 60,601,142 (GRCm39) |
E693D |
probably benign |
Het |
Lrrc37 |
T |
C |
11: 103,511,855 (GRCm39) |
T38A |
unknown |
Het |
Lypd4 |
A |
T |
7: 24,564,254 (GRCm39) |
D201E |
possibly damaging |
Het |
Nin |
A |
G |
12: 70,076,795 (GRCm39) |
S1794P |
|
Het |
Oog2 |
T |
C |
4: 143,920,777 (GRCm39) |
L70P |
probably damaging |
Het |
Or6n2 |
T |
C |
1: 173,897,488 (GRCm39) |
L208P |
probably damaging |
Het |
Pacsin1 |
G |
T |
17: 27,926,034 (GRCm39) |
R282S |
possibly damaging |
Het |
Pcdhb9 |
T |
A |
18: 37,535,361 (GRCm39) |
Y452N |
probably damaging |
Het |
Pdgfra |
T |
C |
5: 75,338,387 (GRCm39) |
V547A |
possibly damaging |
Het |
Plcb4 |
T |
C |
2: 135,781,169 (GRCm39) |
F209L |
probably damaging |
Het |
Pnpla6 |
T |
C |
8: 3,571,384 (GRCm39) |
S158P |
probably benign |
Het |
Prlhr |
C |
G |
19: 60,455,747 (GRCm39) |
R273P |
probably damaging |
Het |
Prss41 |
G |
A |
17: 24,056,607 (GRCm39) |
P196L |
probably damaging |
Het |
Ptgr3 |
T |
C |
18: 84,112,651 (GRCm39) |
L109P |
probably benign |
Het |
Ptpn22 |
A |
G |
3: 103,793,643 (GRCm39) |
E598G |
possibly damaging |
Het |
Rasal2 |
T |
C |
1: 156,992,240 (GRCm39) |
D569G |
possibly damaging |
Het |
Sf3b3 |
A |
C |
8: 111,547,483 (GRCm39) |
M715R |
possibly damaging |
Het |
Ska1 |
T |
C |
18: 74,339,907 (GRCm39) |
N13S |
probably benign |
Het |
Spocd1 |
A |
C |
4: 129,823,497 (GRCm39) |
E98A |
|
Het |
Syf2 |
C |
T |
4: 134,664,182 (GRCm39) |
R199C |
probably damaging |
Het |
Syne2 |
A |
G |
12: 76,108,442 (GRCm39) |
D942G |
possibly damaging |
Het |
Tamalin |
T |
A |
15: 101,129,790 (GRCm39) |
C358S |
possibly damaging |
Het |
Tmem63a |
A |
G |
1: 180,801,776 (GRCm39) |
T764A |
probably benign |
Het |
Ttf1 |
C |
T |
2: 28,957,238 (GRCm39) |
Q503* |
probably null |
Het |
Usp13 |
T |
C |
3: 32,949,025 (GRCm39) |
V454A |
possibly damaging |
Het |
Usp47 |
A |
G |
7: 111,652,472 (GRCm39) |
T50A |
possibly damaging |
Het |
Zfyve26 |
A |
T |
12: 79,315,331 (GRCm39) |
C1382S |
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 |
|
R8109:Sycp1
|
UTSW |
3 |
102,758,918 (GRCm39) |
missense |
probably benign |
0.21 |
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'- ACATACAAAGTGTAAGGCATGC -3'
(R):5'- ACGTACACACCTCTGTCACG -3'
Sequencing Primer
(F):5'- ACAAAGTGTAAGGCATGCTTTTC -3'
(R):5'- TGCAGGCTTTCACCGTG -3'
|
Posted On |
2020-06-30 |