Incidental Mutation 'R9020:Sycp1'
ID |
686644 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Sycp1
|
Ensembl Gene |
ENSMUSG00000027855 |
Gene Name |
synaptonemal complex protein 1 |
Synonyms |
SCP1 |
MMRRC Submission |
068850-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.539)
|
Stock # |
R9020 (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 C
at 102783653 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Lysine to Arginine
at position 607
(K607R)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000029448
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000196988]
|
AlphaFold |
Q62209 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000029448
AA Change: K607R
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
SMART Domains |
Protein: ENSMUSP00000029448 Gene: ENSMUSG00000027855 AA Change: K607R
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000196988
AA Change: K607R
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
SMART Domains |
Protein: ENSMUSP00000143651 Gene: ENSMUSG00000027855 AA Change: K607R
Domain | Start | End | E-Value | Type |
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 98.9%
|
Validation Efficiency |
97% (58/60) |
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: 58 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acot11 |
A |
G |
4: 106,605,615 (GRCm39) |
S586P |
probably damaging |
Het |
Adora3 |
T |
A |
3: 105,815,141 (GRCm39) |
I297N |
probably damaging |
Het |
Adrb3 |
A |
T |
8: 27,717,947 (GRCm39) |
F167L |
probably damaging |
Het |
Apob |
A |
G |
12: 8,063,999 (GRCm39) |
Y3955C |
probably damaging |
Het |
Atp2a1 |
T |
C |
7: 126,046,135 (GRCm39) |
D963G |
probably benign |
Het |
Btbd10 |
T |
C |
7: 112,951,057 (GRCm39) |
N11S |
possibly damaging |
Het |
Casr |
A |
G |
16: 36,315,611 (GRCm39) |
S820P |
probably damaging |
Het |
Ccdc82 |
C |
T |
9: 13,281,915 (GRCm39) |
R447C |
probably damaging |
Het |
Cfap44 |
T |
A |
16: 44,257,522 (GRCm39) |
V1019E |
probably damaging |
Het |
Cfap65 |
T |
C |
1: 74,959,552 (GRCm39) |
E866G |
probably damaging |
Het |
Chd4 |
T |
A |
6: 125,084,469 (GRCm39) |
D713E |
probably damaging |
Het |
Ctdsp1 |
T |
C |
1: 74,434,676 (GRCm39) |
F240S |
possibly damaging |
Het |
Cyp26b1 |
C |
T |
6: 84,552,056 (GRCm39) |
V361I |
probably benign |
Het |
Dmbt1 |
T |
A |
7: 130,712,787 (GRCm39) |
I1597N |
possibly damaging |
Het |
Dnajc25 |
C |
A |
4: 59,003,470 (GRCm39) |
Y80* |
probably null |
Het |
Fbxo17 |
A |
T |
7: 28,436,782 (GRCm39) |
N246Y |
possibly damaging |
Het |
Filip1l |
A |
G |
16: 57,391,058 (GRCm39) |
T549A |
probably benign |
Het |
Gm9758 |
A |
C |
5: 14,964,739 (GRCm39) |
N35K |
|
Het |
Gtf2i |
T |
C |
5: 134,275,415 (GRCm39) |
T707A |
probably benign |
Het |
Ifnk |
T |
C |
4: 35,152,573 (GRCm39) |
V167A |
probably damaging |
Het |
Iqch |
T |
C |
9: 63,432,526 (GRCm39) |
M290V |
probably benign |
Het |
Irx1 |
A |
T |
13: 72,111,548 (GRCm39) |
Y20* |
probably null |
Het |
Jade2 |
T |
A |
11: 51,708,454 (GRCm39) |
Q572L |
probably benign |
Het |
Kcne4 |
T |
A |
1: 78,795,425 (GRCm39) |
H24Q |
probably benign |
Het |
Kcnq5 |
T |
C |
1: 21,539,463 (GRCm39) |
|
probably benign |
Het |
Kcnt2 |
T |
A |
1: 140,512,049 (GRCm39) |
V1068E |
probably benign |
Het |
Klk1b27 |
T |
A |
7: 43,705,118 (GRCm39) |
V95D |
probably damaging |
Het |
Lins1 |
A |
G |
7: 66,357,961 (GRCm39) |
D32G |
probably damaging |
Het |
Mavs |
A |
G |
2: 131,088,594 (GRCm39) |
E466G |
possibly damaging |
Het |
Mipep |
T |
A |
14: 61,068,677 (GRCm39) |
L483* |
probably null |
Het |
Muc16 |
G |
GAATGGCTTTCTT |
9: 18,550,015 (GRCm39) |
|
probably benign |
Het |
Myo1a |
C |
A |
10: 127,549,992 (GRCm39) |
Q491K |
probably benign |
Het |
Nle1 |
C |
G |
11: 82,797,275 (GRCm39) |
E146Q |
probably benign |
Het |
Nphp3 |
T |
C |
9: 103,909,150 (GRCm39) |
Y787H |
probably benign |
Het |
Pcdh15 |
A |
G |
10: 74,481,443 (GRCm39) |
S263G |
probably benign |
Het |
Pcdhb8 |
T |
G |
18: 37,489,837 (GRCm39) |
I505S |
probably damaging |
Het |
Phtf1 |
C |
G |
3: 103,898,694 (GRCm39) |
S339* |
probably null |
Het |
Pip5k1b |
T |
A |
19: 24,327,585 (GRCm39) |
I424F |
probably benign |
Het |
Plxna4 |
T |
A |
6: 32,211,497 (GRCm39) |
T681S |
possibly damaging |
Het |
Prdm1 |
A |
G |
10: 44,316,036 (GRCm39) |
L700P |
probably damaging |
Het |
Prtg |
C |
T |
9: 72,799,277 (GRCm39) |
T769I |
probably damaging |
Het |
Rasgrf2 |
A |
G |
13: 92,165,146 (GRCm39) |
V340A |
possibly damaging |
Het |
Ros1 |
T |
A |
10: 52,031,023 (GRCm39) |
E548D |
probably benign |
Het |
Rsph10b |
G |
A |
5: 143,922,283 (GRCm39) |
R823Q |
probably benign |
Het |
Scgb1b3 |
A |
G |
7: 31,075,276 (GRCm39) |
E42G |
probably damaging |
Het |
Scyl2 |
T |
C |
10: 89,488,858 (GRCm39) |
N486D |
probably damaging |
Het |
Sdr9c7 |
T |
A |
10: 127,745,659 (GRCm39) |
I257N |
possibly damaging |
Het |
Serpinb9b |
A |
T |
13: 33,223,887 (GRCm39) |
I360F |
probably damaging |
Het |
Slc15a5 |
T |
A |
6: 138,032,704 (GRCm39) |
I217F |
probably benign |
Het |
Steap2 |
T |
C |
5: 5,723,480 (GRCm39) |
S467G |
probably benign |
Het |
Tek |
C |
G |
4: 94,708,339 (GRCm39) |
P350R |
probably benign |
Het |
Tet3 |
T |
C |
6: 83,381,418 (GRCm39) |
D250G |
probably damaging |
Het |
Trip11 |
A |
G |
12: 101,850,770 (GRCm39) |
V1098A |
possibly damaging |
Het |
Tsc2 |
G |
T |
17: 24,845,691 (GRCm39) |
T209K |
probably damaging |
Het |
Ttc6 |
A |
G |
12: 57,752,366 (GRCm39) |
Y1424C |
probably damaging |
Het |
Uchl3 |
A |
T |
14: 101,903,986 (GRCm39) |
K74N |
probably damaging |
Het |
Usp10 |
T |
G |
8: 120,667,904 (GRCm39) |
S68R |
probably benign |
Het |
Wwp1 |
T |
C |
4: 19,650,282 (GRCm39) |
I295V |
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 |
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 |
R9149:Sycp1
|
UTSW |
3 |
102,758,944 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- TGGTGAATCCAGAGTTTCTTCAAAGAA -3'
(R):5'- AGGTAGTTAACAGTCACATAAAGGT -3'
Sequencing Primer
(F):5'- ACTGGCTGCTCTTTCAGAGGAC -3'
(R):5'- GGACAATGAAACAAACTGGATAT -3'
|
Posted On |
2021-11-19 |