Incidental Mutation 'R7037:Sycp1'
| ID |
546754 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp1
|
| Ensembl Gene |
ENSMUSG00000027855 |
| Gene Name |
synaptonemal complex protein 1 |
| Synonyms |
SCP1 |
| MMRRC Submission |
045137-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.539)
|
| Stock # |
R7037 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 102806250 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Aspartic acid
at position 480
(E480D)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000143651
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000196988]
|
| AlphaFold |
Q62209 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000029448
AA Change: E480D
PolyPhen 2
Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: E480D
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000196988
AA Change: E480D
PolyPhen 2
Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: E480D
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Meta Mutation Damage Score |
0.1795 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
| Validation Efficiency |
100% (70/70) |
| 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: 70 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acsm3 |
A |
T |
7: 119,367,266 (GRCm39) |
N33I |
probably damaging |
Het |
| Ahnak2 |
A |
T |
12: 112,740,712 (GRCm39) |
V314D |
probably damaging |
Het |
| Arl14epl |
T |
G |
18: 47,065,510 (GRCm39) |
C92G |
probably benign |
Het |
| Atp6v1h |
T |
A |
1: 5,220,215 (GRCm39) |
M423K |
possibly damaging |
Het |
| Baiap3 |
G |
A |
17: 25,462,814 (GRCm39) |
R1075C |
probably benign |
Het |
| Baz2b |
C |
T |
2: 59,764,014 (GRCm39) |
|
probably null |
Het |
| Bicral |
T |
C |
17: 47,135,560 (GRCm39) |
H550R |
probably benign |
Het |
| C1rl |
A |
G |
6: 124,485,598 (GRCm39) |
Y323C |
probably damaging |
Het |
| Ccr9 |
T |
A |
9: 123,609,036 (GRCm39) |
H239Q |
possibly damaging |
Het |
| Cdh16 |
T |
A |
8: 105,344,267 (GRCm39) |
R91* |
probably null |
Het |
| Coro1c |
A |
G |
5: 113,983,457 (GRCm39) |
F357S |
possibly damaging |
Het |
| Cpsf4 |
G |
A |
5: 145,112,939 (GRCm39) |
R141Q |
possibly damaging |
Het |
| Cryzl2 |
G |
A |
1: 157,298,318 (GRCm39) |
V236I |
probably damaging |
Het |
| Cttnbp2 |
T |
C |
6: 18,435,117 (GRCm39) |
E247G |
probably damaging |
Het |
| Dbr1 |
T |
A |
9: 99,458,621 (GRCm39) |
|
probably null |
Het |
| Dclk1 |
T |
C |
3: 55,370,469 (GRCm39) |
S23P |
probably damaging |
Het |
| Dpyd |
A |
T |
3: 118,692,938 (GRCm39) |
I361F |
probably benign |
Het |
| Elac2 |
A |
G |
11: 64,874,537 (GRCm39) |
E218G |
probably benign |
Het |
| Eml4 |
T |
A |
17: 83,732,756 (GRCm39) |
D136E |
probably benign |
Het |
| Foxred1 |
A |
T |
9: 35,118,844 (GRCm39) |
S223T |
probably benign |
Het |
| Garin5b |
G |
T |
7: 4,761,584 (GRCm39) |
|
probably benign |
Het |
| Gask1a |
G |
T |
9: 121,794,592 (GRCm39) |
V249L |
possibly damaging |
Het |
| Gm11595 |
A |
G |
11: 99,663,474 (GRCm39) |
C69R |
unknown |
Het |
| Gna14 |
A |
T |
19: 16,511,128 (GRCm39) |
H59L |
|
Het |
| H2-Ab1 |
T |
A |
17: 34,486,963 (GRCm39) |
I239N |
probably damaging |
Het |
| Ints7 |
T |
C |
1: 191,351,717 (GRCm39) |
S809P |
probably benign |
Het |
| Itgb4 |
T |
A |
11: 115,896,391 (GRCm39) |
Y1379* |
probably null |
Het |
| Kank1 |
A |
G |
19: 25,407,705 (GRCm39) |
D1233G |
probably damaging |
Het |
| Kif13a |
C |
T |
13: 46,905,931 (GRCm39) |
V671M |
possibly damaging |
Het |
| Lrrc66 |
A |
T |
5: 73,764,504 (GRCm39) |
D846E |
probably benign |
Het |
| Lyst |
A |
G |
13: 13,791,251 (GRCm39) |
H38R |
probably damaging |
Het |
| Mc3r |
T |
C |
2: 172,091,554 (GRCm39) |
F259L |
probably damaging |
Het |
| Med25 |
A |
G |
7: 44,532,206 (GRCm39) |
Y384H |
probably damaging |
Het |
| Met |
A |
T |
6: 17,547,127 (GRCm39) |
|
probably benign |
Het |
| Mmp16 |
T |
C |
4: 18,116,148 (GRCm39) |
V584A |
possibly damaging |
Het |
| Mrgprb3 |
A |
G |
7: 48,292,942 (GRCm39) |
L203P |
probably damaging |
Het |
| Mus81 |
A |
G |
19: 5,536,108 (GRCm39) |
L185P |
probably damaging |
Het |
| Naaa |
A |
G |
5: 92,424,934 (GRCm39) |
V75A |
possibly damaging |
Het |
| Obscn |
T |
A |
11: 58,934,755 (GRCm39) |
T5292S |
probably damaging |
Het |
| Obscn |
T |
C |
11: 58,943,430 (GRCm39) |
S4801G |
probably damaging |
Het |
| Or2ag19 |
T |
C |
7: 106,444,543 (GRCm39) |
S242P |
probably damaging |
Het |
| Otof |
T |
C |
5: 30,538,882 (GRCm39) |
D1112G |
probably benign |
Het |
| Pals1 |
T |
A |
12: 78,843,973 (GRCm39) |
I59N |
probably damaging |
Het |
| Pbx4 |
A |
G |
8: 70,317,525 (GRCm39) |
R170G |
probably damaging |
Het |
| Pigt |
CCAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGATCTGTAACCACAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGATCTGTAACCACAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGAT |
CCAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGATCTGTAACCACAGGCCAGTGAGTAGGTTTGTCTCTGTCTAGTGTGGAT |
2: 164,341,589 (GRCm39) |
|
probably null |
Het |
| Plce1 |
A |
T |
19: 38,690,461 (GRCm39) |
D715V |
probably damaging |
Het |
| Pms1 |
T |
C |
1: 53,246,770 (GRCm39) |
T311A |
possibly damaging |
Het |
| Popdc2 |
A |
G |
16: 38,194,629 (GRCm39) |
D350G |
probably damaging |
Het |
| Prex1 |
A |
G |
2: 166,429,100 (GRCm39) |
V661A |
probably benign |
Het |
| Ptbp2 |
A |
G |
3: 119,545,557 (GRCm39) |
Y130H |
probably damaging |
Het |
| Rev3l |
C |
T |
10: 39,727,971 (GRCm39) |
R2707W |
probably damaging |
Het |
| Rpl37 |
G |
A |
15: 5,147,185 (GRCm39) |
R75K |
probably null |
Het |
| Ryr3 |
T |
A |
2: 112,779,475 (GRCm39) |
R259* |
probably null |
Het |
| Scai |
A |
T |
2: 39,080,633 (GRCm39) |
S8T |
probably benign |
Het |
| Scn4a |
C |
A |
11: 106,211,726 (GRCm39) |
L1430F |
probably damaging |
Het |
| Sema5a |
A |
G |
15: 32,686,993 (GRCm39) |
K1035R |
probably damaging |
Het |
| Siah3 |
A |
G |
14: 75,763,025 (GRCm39) |
H92R |
probably benign |
Het |
| Smc4 |
G |
A |
3: 68,925,528 (GRCm39) |
V342I |
possibly damaging |
Het |
| Spata31d1a |
C |
T |
13: 59,848,138 (GRCm39) |
C1330Y |
possibly damaging |
Het |
| St18 |
C |
A |
1: 6,873,260 (GRCm39) |
H332N |
possibly damaging |
Het |
| Tex14 |
A |
T |
11: 87,388,741 (GRCm39) |
I323F |
probably damaging |
Het |
| Tm7sf2 |
A |
T |
19: 6,114,107 (GRCm39) |
|
probably null |
Het |
| Tmem241 |
G |
T |
18: 12,246,463 (GRCm39) |
H62Q |
probably benign |
Het |
| Tmem54 |
T |
A |
4: 129,004,594 (GRCm39) |
|
probably null |
Het |
| Tomm34 |
A |
G |
2: 163,912,398 (GRCm39) |
L39P |
probably damaging |
Het |
| Triml2 |
T |
A |
8: 43,646,573 (GRCm39) |
V354D |
probably damaging |
Het |
| Usp19 |
T |
C |
9: 108,374,157 (GRCm39) |
I738T |
possibly damaging |
Het |
| Utp25 |
A |
C |
1: 192,803,031 (GRCm39) |
|
probably null |
Het |
| Utrn |
T |
A |
10: 12,702,514 (GRCm39) |
|
probably null |
Het |
| Zfp1005 |
G |
T |
2: 150,108,376 (GRCm39) |
V46F |
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 |
|
|
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'- ACAAAGCACGGTCCTTAAATTTG -3'
(R):5'- GCCAAATTTTCTCCAATGTATTGC -3'
Sequencing Primer
(F):5'- GCTTCAGCTTCCAGAGTACTGAG -3'
(R):5'- GAGACTGTCTATGGAACTCCTGC -3'
|
| Posted On |
2019-05-13 |
Incidental Mutation