Incidental Mutation 'R5576:Sycp1'
| ID |
437200 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp1
|
| Ensembl Gene |
ENSMUSG00000027855 |
| Gene Name |
synaptonemal complex protein 1 |
| Synonyms |
SCP1 |
| MMRRC Submission |
043131-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.539)
|
| Stock # |
R5576 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 102726218 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Glycine
at position 969
(R969G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000143651
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000196988]
|
| AlphaFold |
Q62209 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000029448
AA Change: R969G
PolyPhen 2
Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: R969G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000196988
AA Change: R969G
PolyPhen 2
Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: R969G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000198651
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.4%
- 20x: 95.5%
|
| Validation Efficiency |
|
| 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: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930522L14Rik |
G |
A |
5: 109,885,570 (GRCm39) |
T96I |
probably benign |
Het |
| Add2 |
G |
T |
6: 86,084,457 (GRCm39) |
|
probably null |
Het |
| Agbl1 |
C |
T |
7: 75,984,985 (GRCm39) |
T134M |
probably benign |
Het |
| Agfg1 |
T |
A |
1: 82,848,445 (GRCm39) |
S32T |
probably benign |
Het |
| Ankrd17 |
A |
C |
5: 90,391,083 (GRCm39) |
S2087A |
probably benign |
Het |
| Apob |
A |
T |
12: 8,048,662 (GRCm39) |
E1012V |
probably damaging |
Het |
| Baiap2 |
T |
A |
11: 119,887,737 (GRCm39) |
V297E |
probably benign |
Het |
| BC034090 |
T |
G |
1: 155,117,214 (GRCm39) |
K301N |
probably benign |
Het |
| Bhlha9 |
T |
C |
11: 76,563,595 (GRCm39) |
I74T |
probably damaging |
Het |
| Btnl9 |
T |
C |
11: 49,069,712 (GRCm39) |
H189R |
probably benign |
Het |
| Ccdc122 |
G |
A |
14: 77,329,317 (GRCm39) |
M123I |
probably benign |
Het |
| Cybb |
C |
G |
X: 9,316,989 (GRCm39) |
D246H |
probably benign |
Het |
| Dnah9 |
T |
C |
11: 65,724,922 (GRCm39) |
|
probably null |
Het |
| Dnaja2 |
A |
T |
8: 86,266,033 (GRCm39) |
L351I |
possibly damaging |
Het |
| Efcab6 |
C |
A |
15: 83,834,201 (GRCm39) |
S469I |
probably benign |
Het |
| Esp15 |
C |
A |
17: 39,953,564 (GRCm39) |
T17K |
probably damaging |
Het |
| Fads1 |
A |
G |
19: 10,163,238 (GRCm39) |
T172A |
probably benign |
Het |
| Fbp2 |
A |
T |
13: 62,985,005 (GRCm39) |
D305E |
probably benign |
Het |
| Golga4 |
A |
G |
9: 118,382,602 (GRCm39) |
T541A |
probably benign |
Het |
| Herc3 |
T |
C |
6: 58,865,710 (GRCm39) |
Y768H |
probably benign |
Het |
| Kmt2a |
A |
G |
9: 44,753,931 (GRCm39) |
V514A |
possibly damaging |
Het |
| Melk |
A |
G |
4: 44,312,255 (GRCm39) |
E141G |
probably null |
Het |
| Nln |
A |
G |
13: 104,195,338 (GRCm39) |
Y245H |
probably damaging |
Het |
| Nrap |
C |
T |
19: 56,310,414 (GRCm39) |
R1563H |
probably damaging |
Het |
| Or7g34 |
T |
A |
9: 19,478,369 (GRCm39) |
M101L |
probably benign |
Het |
| Or8b44 |
A |
C |
9: 38,410,204 (GRCm39) |
K80Q |
probably damaging |
Het |
| Pde4b |
T |
A |
4: 102,287,359 (GRCm39) |
I34N |
probably damaging |
Het |
| Pex11g |
A |
G |
8: 3,515,875 (GRCm39) |
S53P |
probably damaging |
Het |
| Pole |
A |
T |
5: 110,459,931 (GRCm39) |
K1112* |
probably null |
Het |
| Ppfia4 |
T |
G |
1: 134,250,788 (GRCm39) |
D184A |
possibly damaging |
Het |
| Rpp30 |
T |
A |
19: 36,079,251 (GRCm39) |
D216E |
probably benign |
Het |
| Sbno2 |
C |
T |
10: 79,903,171 (GRCm39) |
A398T |
probably damaging |
Het |
| Sbp |
T |
A |
17: 24,164,552 (GRCm39) |
S94T |
probably benign |
Het |
| Skp1 |
T |
G |
11: 52,133,415 (GRCm39) |
D33E |
possibly damaging |
Het |
| Slc17a8 |
A |
G |
10: 89,433,364 (GRCm39) |
W220R |
probably damaging |
Het |
| Slfn9 |
A |
T |
11: 82,872,258 (GRCm39) |
M826K |
probably benign |
Het |
| Snx2 |
A |
G |
18: 53,343,822 (GRCm39) |
K322E |
probably benign |
Het |
| Spata32 |
T |
A |
11: 103,100,653 (GRCm39) |
N38I |
possibly damaging |
Het |
| Trgc2 |
T |
C |
13: 19,489,301 (GRCm39) |
I144V |
probably benign |
Het |
| Trpc1 |
A |
G |
9: 95,603,377 (GRCm39) |
L385S |
probably damaging |
Het |
| Vmn2r105 |
C |
T |
17: 20,444,836 (GRCm39) |
|
probably null |
Het |
| Xrcc6 |
T |
A |
15: 81,906,693 (GRCm39) |
D79E |
probably damaging |
Het |
| Zan |
A |
T |
5: 137,426,744 (GRCm39) |
C2467* |
probably null |
Het |
| Zfp26 |
A |
G |
9: 20,348,803 (GRCm39) |
V587A |
possibly damaging |
Het |
| Zfp553 |
C |
T |
7: 126,835,875 (GRCm39) |
R477C |
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 |
|
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'- TGATTAACTATTCAGAGACCCTCAC -3'
(R):5'- GAGCCTGGTTTCAGAGGAAG -3'
Sequencing Primer
(F):5'- CTTCGAACTTCAATATCCATTGCAAG -3'
(R):5'- AGCCTGGTTTCAGAGGAAGATGTATC -3'
|
| Posted On |
2016-10-26 |
Incidental Mutation