Incidental Mutation 'R6460:Sycp1'
ID |
517551 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Sycp1
|
Ensembl Gene |
ENSMUSG00000027855 |
Gene Name |
synaptonemal complex protein 1 |
Synonyms |
SCP1 |
MMRRC Submission |
044595-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.539)
|
Stock # |
R6460 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
3 |
Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to G
at 102832569 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Tyrosine to Serine
at position 199
(Y199S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000143651
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000196988]
[ENSMUST00000199930]
|
AlphaFold |
Q62209 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000029448
AA Change: Y199S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000029448 Gene: ENSMUSG00000027855 AA Change: Y199S
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000196988
AA Change: Y199S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000143651 Gene: ENSMUSG00000027855 AA Change: Y199S
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000199930
AA Change: Y144S
PolyPhen 2
Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000143493 Gene: ENSMUSG00000027855 AA Change: Y144S
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: 99.9%
- 3x: 99.6%
- 10x: 97.9%
- 20x: 93.8%
|
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: 54 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca7 |
A |
T |
10: 79,844,862 (GRCm39) |
H1528L |
probably benign |
Het |
Ablim1 |
A |
G |
19: 57,068,271 (GRCm39) |
S263P |
possibly damaging |
Het |
Ahnak2 |
T |
C |
12: 112,750,610 (GRCm39) |
E104G |
probably null |
Het |
Apof |
T |
A |
10: 128,105,086 (GRCm39) |
M80K |
probably damaging |
Het |
Arfgef1 |
C |
T |
1: 10,283,285 (GRCm39) |
R208H |
probably damaging |
Het |
Arhgef33 |
A |
G |
17: 80,657,018 (GRCm39) |
|
probably null |
Het |
Atxn2l |
CCAGCAGCAGCAGCAGCAGC |
CCAGCAGCAGCAGCAGC |
7: 126,093,420 (GRCm39) |
|
probably benign |
Het |
Cabcoco1 |
T |
C |
10: 68,352,211 (GRCm39) |
K34E |
probably damaging |
Het |
Col4a4 |
C |
A |
1: 82,444,253 (GRCm39) |
G1338V |
unknown |
Het |
Coq9 |
T |
A |
8: 95,579,814 (GRCm39) |
D256E |
probably damaging |
Het |
Dnajc18 |
A |
T |
18: 35,833,963 (GRCm39) |
C41S |
probably benign |
Het |
Dnajc6 |
A |
G |
4: 101,472,795 (GRCm39) |
I307M |
probably damaging |
Het |
Emg1 |
A |
G |
6: 124,688,870 (GRCm39) |
V46A |
probably damaging |
Het |
Eya3 |
A |
G |
4: 132,408,174 (GRCm39) |
S157G |
probably damaging |
Het |
Eya4 |
T |
C |
10: 23,027,910 (GRCm39) |
N274S |
probably benign |
Het |
Fan1 |
T |
A |
7: 64,022,234 (GRCm39) |
N340Y |
probably damaging |
Het |
Fat3 |
A |
G |
9: 15,878,296 (GRCm39) |
V3395A |
probably damaging |
Het |
Fchsd1 |
A |
T |
18: 38,092,897 (GRCm39) |
|
probably null |
Het |
Gm4846 |
A |
G |
1: 166,325,082 (GRCm39) |
V3A |
probably benign |
Het |
Hecw2 |
T |
A |
1: 53,907,992 (GRCm39) |
|
probably null |
Het |
Herc3 |
T |
A |
6: 58,867,108 (GRCm39) |
I10N |
probably damaging |
Het |
Hhatl |
C |
T |
9: 121,618,588 (GRCm39) |
R138H |
probably benign |
Het |
Hspa9 |
A |
T |
18: 35,085,765 (GRCm39) |
H35Q |
probably benign |
Het |
Irgq |
T |
A |
7: 24,233,115 (GRCm39) |
S319T |
probably benign |
Het |
Kif1b |
T |
C |
4: 149,277,053 (GRCm39) |
M1337V |
probably benign |
Het |
Ksr2 |
T |
A |
5: 117,894,449 (GRCm39) |
|
probably null |
Het |
Lrriq1 |
T |
C |
10: 103,036,559 (GRCm39) |
I865V |
probably damaging |
Het |
Map2k1 |
A |
G |
9: 64,094,577 (GRCm39) |
L355P |
probably damaging |
Het |
Muc16 |
A |
G |
9: 18,551,812 (GRCm39) |
I4827T |
probably benign |
Het |
Myh1 |
T |
C |
11: 67,112,202 (GRCm39) |
V1752A |
probably benign |
Het |
Nfatc2ip |
A |
G |
7: 125,986,909 (GRCm39) |
V282A |
probably damaging |
Het |
Nrg1 |
T |
A |
8: 32,308,561 (GRCm39) |
E485V |
probably damaging |
Het |
Ofcc1 |
T |
C |
13: 40,441,455 (GRCm39) |
D2G |
probably damaging |
Het |
Or10d3 |
CAGAG |
CAG |
9: 39,462,088 (GRCm39) |
|
probably null |
Het |
Pclo |
T |
C |
5: 14,729,146 (GRCm39) |
|
probably benign |
Het |
Pom121 |
T |
C |
5: 135,420,537 (GRCm39) |
K295E |
unknown |
Het |
Rb1 |
A |
C |
14: 73,515,894 (GRCm39) |
I294R |
probably benign |
Het |
Schip1 |
C |
A |
3: 68,402,227 (GRCm39) |
S101R |
probably benign |
Het |
Sec24c |
T |
A |
14: 20,740,868 (GRCm39) |
Y629N |
probably damaging |
Het |
Shkbp1 |
T |
A |
7: 27,049,963 (GRCm39) |
H305L |
probably benign |
Het |
Spag9 |
T |
C |
11: 93,959,801 (GRCm39) |
I187T |
probably damaging |
Het |
Srp72 |
C |
A |
5: 77,135,838 (GRCm39) |
T256K |
probably damaging |
Het |
Stk32c |
T |
A |
7: 138,685,190 (GRCm39) |
N320I |
probably damaging |
Het |
Stxbp4 |
A |
T |
11: 90,497,811 (GRCm39) |
S163T |
probably benign |
Het |
Tpk1 |
T |
C |
6: 43,445,961 (GRCm39) |
D159G |
probably benign |
Het |
Trav21-dv12 |
C |
T |
14: 54,114,191 (GRCm39) |
H104Y |
probably benign |
Het |
Trip4 |
A |
T |
9: 65,788,302 (GRCm39) |
Y48N |
probably damaging |
Het |
Trmt10b |
A |
G |
4: 45,314,322 (GRCm39) |
T255A |
possibly damaging |
Het |
Ttn |
G |
A |
2: 76,747,232 (GRCm39) |
Q4606* |
probably null |
Het |
Vcan |
T |
A |
13: 89,838,806 (GRCm39) |
K2246M |
possibly damaging |
Het |
Zfp438 |
C |
A |
18: 5,213,603 (GRCm39) |
G452C |
probably damaging |
Het |
Zfp54 |
T |
A |
17: 21,654,004 (GRCm39) |
I166N |
probably benign |
Het |
Zfp735 |
T |
C |
11: 73,602,478 (GRCm39) |
V474A |
probably benign |
Het |
Zfp831 |
G |
T |
2: 174,488,360 (GRCm39) |
G1012W |
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 |
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'- GGTGATTCAACCATGCATCAATAA -3'
(R):5'- CAGGCCAGTGAGTTTATGATTTT -3'
Sequencing Primer
(F):5'- AGCTATCACTCTTTCTGCTTAG -3'
(R):5'- GCAATGCCAGTTACAGTTCAG -3'
|
Posted On |
2018-05-21 |