Incidental Mutation 'R5079:Sycp1'
ID |
387007 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Sycp1
|
Ensembl Gene |
ENSMUSG00000027855 |
Gene Name |
synaptonemal complex protein 1 |
Synonyms |
SCP1 |
MMRRC Submission |
042668-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.539)
|
Stock # |
R5079 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 102786116 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Cysteine to Arginine
at position 589
(C589R)
|
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: C589R
PolyPhen 2
Score 0.666 (Sensitivity: 0.86; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000029448 Gene: ENSMUSG00000027855 AA Change: C589R
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000196911
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000196988
AA Change: C589R
PolyPhen 2
Score 0.666 (Sensitivity: 0.86; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000143651 Gene: ENSMUSG00000027855 AA Change: C589R
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Meta Mutation Damage Score |
0.0884 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.1%
- 20x: 91.6%
|
Validation Efficiency |
90% (63/70) |
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: 59 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930522L14Rik |
T |
C |
5: 109,885,196 (GRCm39) |
S221G |
probably benign |
Het |
Abca9 |
A |
T |
11: 110,036,395 (GRCm39) |
F571L |
possibly damaging |
Het |
Agbl4 |
T |
A |
4: 111,423,826 (GRCm39) |
M284K |
possibly damaging |
Het |
Ankrd16 |
A |
G |
2: 11,783,710 (GRCm39) |
D104G |
probably damaging |
Het |
Bpifc |
T |
C |
10: 85,817,168 (GRCm39) |
D230G |
probably damaging |
Het |
Casc3 |
C |
T |
11: 98,701,252 (GRCm39) |
|
probably benign |
Het |
Catsperd |
T |
C |
17: 56,965,153 (GRCm39) |
|
probably null |
Het |
Cpxm2 |
C |
T |
7: 131,756,014 (GRCm39) |
|
probably null |
Het |
Crisp1 |
A |
T |
17: 40,619,867 (GRCm39) |
|
probably null |
Het |
Crybg2 |
T |
C |
4: 133,801,564 (GRCm39) |
I908T |
possibly damaging |
Het |
Csn3 |
T |
C |
5: 88,077,626 (GRCm39) |
V44A |
possibly damaging |
Het |
Dipk1c |
A |
T |
18: 84,748,702 (GRCm39) |
H100L |
probably benign |
Het |
Dop1a |
T |
A |
9: 86,369,474 (GRCm39) |
D102E |
probably damaging |
Het |
Etfdh |
T |
C |
3: 79,525,705 (GRCm39) |
Y111C |
probably damaging |
Het |
Fat3 |
T |
C |
9: 15,910,423 (GRCm39) |
S1860G |
probably benign |
Het |
Gba2 |
G |
T |
4: 43,568,640 (GRCm39) |
|
probably benign |
Het |
Ggta1 |
A |
G |
2: 35,312,249 (GRCm39) |
I43T |
possibly damaging |
Het |
Glb1l2 |
T |
C |
9: 26,682,405 (GRCm39) |
I149V |
probably benign |
Het |
Gm5084 |
T |
A |
13: 60,360,639 (GRCm39) |
|
noncoding transcript |
Het |
Gm5591 |
G |
T |
7: 38,221,560 (GRCm39) |
P170T |
probably benign |
Het |
Gucy2d |
A |
T |
7: 98,107,475 (GRCm39) |
|
probably null |
Het |
Itpr3 |
T |
C |
17: 27,317,397 (GRCm39) |
F851L |
probably damaging |
Het |
Kat2b |
T |
A |
17: 53,970,666 (GRCm39) |
I684N |
probably damaging |
Het |
Klra17 |
C |
A |
6: 129,849,159 (GRCm39) |
K138N |
possibly damaging |
Het |
Lrrc4 |
T |
A |
6: 28,830,769 (GRCm39) |
H282L |
possibly damaging |
Het |
Lyst |
T |
C |
13: 13,931,938 (GRCm39) |
I3522T |
probably benign |
Het |
Man2c1 |
A |
G |
9: 57,044,000 (GRCm39) |
T312A |
probably damaging |
Het |
Mapkbp1 |
A |
G |
2: 119,844,214 (GRCm39) |
R313G |
probably damaging |
Het |
N4bp2 |
G |
A |
5: 65,969,320 (GRCm39) |
G1361R |
probably damaging |
Het |
Nbas |
A |
T |
12: 13,424,712 (GRCm39) |
I984F |
probably damaging |
Het |
Ncor1 |
T |
A |
11: 62,236,063 (GRCm39) |
Q579L |
possibly damaging |
Het |
Nme9 |
A |
G |
9: 99,341,755 (GRCm39) |
Y35C |
probably damaging |
Het |
Or5w13 |
C |
A |
2: 87,523,552 (GRCm39) |
V225F |
probably damaging |
Het |
Ormdl1 |
T |
C |
1: 53,348,093 (GRCm39) |
V145A |
probably damaging |
Het |
Paxbp1 |
C |
A |
16: 90,822,034 (GRCm39) |
|
probably null |
Het |
Pcnx1 |
C |
A |
12: 82,025,863 (GRCm39) |
S1530* |
probably null |
Het |
Pogk |
A |
G |
1: 166,226,733 (GRCm39) |
W473R |
probably damaging |
Het |
Pot1b |
A |
T |
17: 55,976,801 (GRCm39) |
S374T |
probably benign |
Het |
Rcn1 |
A |
G |
2: 105,229,402 (GRCm39) |
F50S |
probably damaging |
Het |
Rcvrn |
T |
A |
11: 67,593,767 (GRCm39) |
I186N |
probably damaging |
Het |
Rnd2 |
C |
T |
11: 101,359,825 (GRCm39) |
L57F |
probably damaging |
Het |
Ror1 |
T |
A |
4: 100,298,619 (GRCm39) |
I664N |
probably damaging |
Het |
Sall2 |
G |
T |
14: 52,552,211 (GRCm39) |
A326E |
probably damaging |
Het |
Sh2d6 |
G |
A |
6: 72,496,833 (GRCm39) |
P66S |
probably benign |
Het |
Slc6a20b |
T |
A |
9: 123,427,563 (GRCm39) |
S449C |
probably damaging |
Het |
Slc9a3 |
A |
T |
13: 74,312,406 (GRCm39) |
N668Y |
probably damaging |
Het |
Slco1a8 |
A |
C |
6: 141,918,073 (GRCm39) |
I601R |
probably benign |
Het |
Sorcs2 |
T |
G |
5: 36,200,796 (GRCm39) |
K584T |
probably damaging |
Het |
Stam |
T |
C |
2: 14,079,350 (GRCm39) |
M8T |
probably benign |
Het |
Styk1 |
G |
A |
6: 131,278,676 (GRCm39) |
P333S |
probably damaging |
Het |
Tas2r123 |
A |
G |
6: 132,824,681 (GRCm39) |
I193V |
probably benign |
Het |
Tnks1bp1 |
C |
A |
2: 84,892,970 (GRCm39) |
Q304K |
probably damaging |
Het |
Traf3ip2 |
T |
C |
10: 39,502,473 (GRCm39) |
L207P |
probably damaging |
Het |
Usp49 |
A |
G |
17: 47,984,146 (GRCm39) |
S384G |
possibly damaging |
Het |
Vezt |
T |
C |
10: 93,856,486 (GRCm39) |
|
probably null |
Het |
Vmn1r87 |
C |
A |
7: 12,866,253 (GRCm39) |
M11I |
probably benign |
Het |
Vmn2r39 |
A |
G |
7: 9,026,489 (GRCm39) |
V504A |
probably benign |
Het |
Wapl |
G |
A |
14: 34,446,714 (GRCm39) |
A607T |
probably damaging |
Het |
Zfp638 |
A |
G |
6: 83,906,438 (GRCm39) |
N201S |
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 |
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 |
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'- CCCAATTTAGCCTCTATCATTTAAGGA -3'
(R):5'- AGAAATATGCCTATTAATAGACAGGCA -3'
Sequencing Primer
(F):5'- AACTGAACCTGGGGGTCCTTAAC -3'
(R):5'- AGACAGGCATAAAAAGTTACTA -3'
|
Posted On |
2016-06-06 |