Incidental Mutation 'R5393:Sycp1'
ID |
425946 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Sycp1
|
Ensembl Gene |
ENSMUSG00000027855 |
Gene Name |
synaptonemal complex protein 1 |
Synonyms |
SCP1 |
MMRRC Submission |
042965-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.539)
|
Stock # |
R5393 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
Type of Mutation |
splice site |
DNA Base Change (assembly) |
T to C
at 102748363 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000143651
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000196988]
|
AlphaFold |
Q62209 |
Predicted Effect |
probably null
Transcript: ENSMUST00000029448
|
SMART Domains |
Protein: ENSMUSP00000029448 Gene: ENSMUSG00000027855
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Predicted Effect |
probably null
Transcript: ENSMUST00000196988
|
SMART Domains |
Protein: ENSMUSP00000143651 Gene: ENSMUSG00000027855
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Meta Mutation Damage Score |
0.9755 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
Validation Efficiency |
99% (72/73) |
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: 62 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1110025L11Rik |
A |
T |
16: 88,860,653 (GRCm39) |
Y60* |
probably null |
Het |
Abca6 |
T |
A |
11: 110,135,121 (GRCm39) |
E221D |
probably benign |
Het |
Acyp2 |
C |
T |
11: 30,456,354 (GRCm39) |
E98K |
possibly damaging |
Het |
Adi1 |
A |
G |
12: 28,725,274 (GRCm39) |
D8G |
probably benign |
Het |
Adnp |
T |
C |
2: 168,024,869 (GRCm39) |
K809E |
possibly damaging |
Het |
Aldh18a1 |
T |
C |
19: 40,574,011 (GRCm39) |
H4R |
probably benign |
Het |
Atp6v0a1 |
T |
C |
11: 100,929,633 (GRCm39) |
S485P |
possibly damaging |
Het |
C1galt1 |
T |
C |
6: 7,864,143 (GRCm39) |
|
probably null |
Het |
Cacna2d4 |
A |
T |
6: 119,216,015 (GRCm39) |
N94I |
probably benign |
Het |
Catsperg1 |
T |
C |
7: 28,884,924 (GRCm39) |
N899S |
probably damaging |
Het |
Cilk1 |
A |
G |
9: 78,067,997 (GRCm39) |
T463A |
probably benign |
Het |
Coro2a |
A |
G |
4: 46,542,255 (GRCm39) |
S373P |
probably damaging |
Het |
Cpsf6 |
G |
C |
10: 117,197,921 (GRCm39) |
|
probably benign |
Het |
Csmd3 |
A |
T |
15: 47,497,099 (GRCm39) |
N3099K |
probably damaging |
Het |
Ctla2b |
T |
A |
13: 61,043,946 (GRCm39) |
E74D |
probably damaging |
Het |
Dnah2 |
T |
A |
11: 69,391,683 (GRCm39) |
T671S |
probably benign |
Het |
Drd5 |
T |
A |
5: 38,478,248 (GRCm39) |
S414T |
probably benign |
Het |
Dyrk2 |
C |
T |
10: 118,695,753 (GRCm39) |
D502N |
probably damaging |
Het |
Ecel1 |
A |
T |
1: 87,080,598 (GRCm39) |
L376Q |
possibly damaging |
Het |
Efcab8 |
G |
A |
2: 153,622,903 (GRCm39) |
R24Q |
unknown |
Het |
Eloc |
A |
C |
1: 16,718,192 (GRCm39) |
|
probably benign |
Het |
Ep300 |
A |
G |
15: 81,515,819 (GRCm39) |
|
probably benign |
Het |
Fam89b |
T |
C |
19: 5,778,733 (GRCm39) |
D152G |
probably damaging |
Het |
Gm15455 |
G |
A |
1: 33,875,927 (GRCm39) |
|
noncoding transcript |
Het |
Greb1l |
A |
G |
18: 10,458,312 (GRCm39) |
T30A |
probably benign |
Het |
Hdac10 |
T |
C |
15: 89,010,887 (GRCm39) |
Y238C |
probably damaging |
Het |
Ighv2-5 |
T |
C |
12: 113,649,502 (GRCm39) |
T12A |
possibly damaging |
Het |
Insrr |
T |
C |
3: 87,718,007 (GRCm39) |
|
probably null |
Het |
Irf9 |
T |
C |
14: 55,843,914 (GRCm39) |
|
probably benign |
Het |
Itpr2 |
A |
T |
6: 146,277,653 (GRCm39) |
C280* |
probably null |
Het |
Kcnk18 |
T |
C |
19: 59,208,271 (GRCm39) |
C36R |
probably damaging |
Het |
Khdc4 |
T |
A |
3: 88,603,913 (GRCm39) |
H243Q |
probably benign |
Het |
Klhl14 |
G |
T |
18: 21,785,051 (GRCm39) |
N125K |
probably benign |
Het |
Lce1i |
T |
C |
3: 92,685,042 (GRCm39) |
S45G |
unknown |
Het |
Lrmda |
A |
C |
14: 22,077,374 (GRCm39) |
D37A |
probably damaging |
Het |
Marco |
A |
C |
1: 120,413,583 (GRCm39) |
D280E |
probably damaging |
Het |
Meak7 |
T |
C |
8: 120,499,157 (GRCm39) |
I112V |
probably benign |
Het |
Miox |
C |
T |
15: 89,220,450 (GRCm39) |
Q180* |
probably null |
Het |
Npdc1 |
A |
T |
2: 25,298,682 (GRCm39) |
M265L |
probably damaging |
Het |
Nudcd3 |
T |
C |
11: 6,063,274 (GRCm39) |
K205R |
probably damaging |
Het |
Or2ak6 |
T |
A |
11: 58,593,326 (GRCm39) |
H266Q |
probably damaging |
Het |
Or2t46 |
C |
G |
11: 58,471,825 (GRCm39) |
L52V |
possibly damaging |
Het |
Pcdhga5 |
C |
T |
18: 37,829,720 (GRCm39) |
R723C |
probably benign |
Het |
Pdlim5 |
T |
A |
3: 141,964,947 (GRCm39) |
E295D |
probably damaging |
Het |
Poli |
C |
A |
18: 70,650,499 (GRCm39) |
E314* |
probably null |
Het |
Ptpro |
A |
G |
6: 137,357,222 (GRCm39) |
N238D |
probably benign |
Het |
R3hdm1 |
A |
G |
1: 128,159,084 (GRCm39) |
I920V |
probably benign |
Het |
Ralgapa2 |
C |
T |
2: 146,187,375 (GRCm39) |
V1338M |
probably damaging |
Het |
Saa3 |
T |
C |
7: 46,362,085 (GRCm39) |
Y53C |
probably damaging |
Het |
Septin14 |
T |
A |
5: 129,760,650 (GRCm39) |
E398D |
probably benign |
Het |
Six3 |
T |
C |
17: 85,931,270 (GRCm39) |
S309P |
possibly damaging |
Het |
Slc7a14 |
A |
G |
3: 31,311,919 (GRCm39) |
S34P |
probably damaging |
Het |
Smarca2 |
C |
A |
19: 26,617,829 (GRCm39) |
Q287K |
probably benign |
Het |
Stard9 |
C |
T |
2: 120,533,387 (GRCm39) |
L522F |
possibly damaging |
Het |
Tbc1d8 |
A |
T |
1: 39,465,169 (GRCm39) |
V73E |
probably damaging |
Het |
Tmem120a |
T |
C |
5: 135,765,104 (GRCm39) |
|
probably null |
Het |
Tsc2 |
T |
C |
17: 24,819,370 (GRCm39) |
E1251G |
possibly damaging |
Het |
Vps51 |
T |
G |
19: 6,121,063 (GRCm39) |
E283D |
probably benign |
Het |
Wnt5b |
A |
C |
6: 119,417,394 (GRCm39) |
L157R |
probably damaging |
Het |
Zbtb24 |
T |
A |
10: 41,340,578 (GRCm39) |
V536E |
probably damaging |
Het |
Zfp593 |
G |
A |
4: 133,972,615 (GRCm39) |
A67V |
probably benign |
Het |
Zfp995 |
A |
T |
17: 22,099,473 (GRCm39) |
F254I |
probably benign |
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 |
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 |
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'- TTTCATGCTGAAAGGTCTTTGC -3'
(R):5'- TTTCTCACAATTGGAGCAGATGCC -3'
Sequencing Primer
(F):5'- CTTTGTAACTGTTGTAGGTAAAATGC -3'
(R):5'- GAGCAGATGCCCATTTTTCAG -3'
|
Posted On |
2016-08-04 |