Incidental Mutation 'R6527:Sycp1'
| ID |
521942 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp1
|
| Ensembl Gene |
ENSMUSG00000027855 |
| Gene Name |
synaptonemal complex protein 1 |
| Synonyms |
SCP1 |
| MMRRC Submission |
044653-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.539)
|
| Stock # |
R6527 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 102806203 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 496
(V496A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000143651
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000196988]
|
| AlphaFold |
Q62209 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029448
AA Change: V496A
PolyPhen 2
Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: V496A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000196988
AA Change: V496A
PolyPhen 2
Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: V496A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.9%
- 20x: 93.7%
|
| 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: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
A |
G |
3: 137,773,288 (GRCm39) |
T826A |
probably damaging |
Het |
| Abca16 |
T |
A |
7: 120,076,995 (GRCm39) |
I686N |
possibly damaging |
Het |
| Abcb6 |
T |
C |
1: 75,154,132 (GRCm39) |
|
probably null |
Het |
| Adgrl3 |
A |
C |
5: 81,935,364 (GRCm39) |
E1299A |
probably damaging |
Het |
| Amd2 |
A |
C |
10: 35,586,802 (GRCm39) |
Y252D |
probably damaging |
Het |
| Cfap74 |
A |
G |
4: 155,506,722 (GRCm39) |
|
probably null |
Het |
| Dhx29 |
G |
T |
13: 113,069,076 (GRCm39) |
K135N |
probably damaging |
Het |
| Dlg5 |
T |
A |
14: 24,240,516 (GRCm39) |
D245V |
possibly damaging |
Het |
| Dscaml1 |
C |
T |
9: 45,623,482 (GRCm39) |
Q83* |
probably null |
Het |
| Dsp |
T |
A |
13: 38,379,849 (GRCm39) |
L1599Q |
probably damaging |
Het |
| Duox2 |
A |
G |
2: 122,125,095 (GRCm39) |
V369A |
probably benign |
Het |
| Flacc1 |
T |
C |
1: 58,731,572 (GRCm39) |
M1V |
probably null |
Het |
| Gbe1 |
T |
A |
16: 70,230,560 (GRCm39) |
|
probably null |
Het |
| Gm7298 |
A |
G |
6: 121,746,669 (GRCm39) |
K600R |
probably benign |
Het |
| Heatr4 |
C |
T |
12: 84,026,537 (GRCm39) |
G240E |
probably damaging |
Het |
| Jakmip2 |
A |
G |
18: 43,689,589 (GRCm39) |
V651A |
possibly damaging |
Het |
| Jam3 |
C |
T |
9: 27,066,640 (GRCm39) |
R8Q |
unknown |
Het |
| Letm2 |
A |
G |
8: 26,082,522 (GRCm39) |
|
probably benign |
Het |
| Lmod3 |
T |
C |
6: 97,224,339 (GRCm39) |
D494G |
probably benign |
Het |
| Mast2 |
T |
C |
4: 116,172,136 (GRCm39) |
D604G |
probably damaging |
Het |
| Mif4gd |
C |
T |
11: 115,500,101 (GRCm39) |
|
probably null |
Het |
| Msr1 |
T |
C |
8: 40,077,274 (GRCm39) |
E112G |
possibly damaging |
Het |
| Mtus2 |
A |
G |
5: 148,214,408 (GRCm39) |
|
probably null |
Het |
| Muc4 |
A |
G |
16: 32,753,433 (GRCm38) |
H1103R |
probably benign |
Het |
| Nudt14 |
T |
A |
12: 112,898,507 (GRCm39) |
I198F |
possibly damaging |
Het |
| Or11j4 |
T |
A |
14: 50,630,885 (GRCm39) |
L224* |
probably null |
Het |
| Or13p3 |
T |
A |
4: 118,567,045 (GRCm39) |
F147Y |
possibly damaging |
Het |
| Or1n1b |
T |
C |
2: 36,780,594 (GRCm39) |
T89A |
probably benign |
Het |
| Osbpl8 |
T |
C |
10: 111,129,066 (GRCm39) |
I884T |
probably benign |
Het |
| Podxl2 |
T |
C |
6: 88,819,912 (GRCm39) |
N550S |
probably damaging |
Het |
| Ppp1r9a |
A |
G |
6: 5,045,949 (GRCm39) |
Y151C |
probably damaging |
Het |
| Prss42 |
T |
C |
9: 110,629,924 (GRCm39) |
V226A |
possibly damaging |
Het |
| Psmd12 |
A |
G |
11: 107,379,794 (GRCm39) |
I116V |
probably damaging |
Het |
| Psme4 |
A |
C |
11: 30,782,175 (GRCm39) |
I872L |
probably benign |
Het |
| Rab11fip1 |
A |
T |
8: 27,664,420 (GRCm39) |
V65E |
probably damaging |
Het |
| Ros1 |
T |
C |
10: 52,019,473 (GRCm39) |
N700S |
possibly damaging |
Het |
| Slc15a4 |
G |
A |
5: 127,673,773 (GRCm39) |
T547M |
probably damaging |
Het |
| Slfn3 |
T |
A |
11: 83,103,932 (GRCm39) |
C268S |
probably benign |
Het |
| Smc5 |
T |
C |
19: 23,205,554 (GRCm39) |
Q794R |
probably benign |
Het |
| Sqor |
A |
G |
2: 122,651,206 (GRCm39) |
Y434C |
probably damaging |
Het |
| Steap4 |
T |
A |
5: 8,028,502 (GRCm39) |
L360H |
probably damaging |
Het |
| Tmem161b |
T |
G |
13: 84,420,383 (GRCm39) |
M128R |
probably benign |
Het |
| Tmem59l |
T |
C |
8: 70,938,775 (GRCm39) |
E102G |
probably damaging |
Het |
| Tnks |
A |
T |
8: 35,340,247 (GRCm39) |
V457D |
probably benign |
Het |
| Tomt |
A |
G |
7: 101,549,599 (GRCm39) |
Y230H |
probably damaging |
Het |
| Trim37 |
A |
G |
11: 87,080,910 (GRCm39) |
N561D |
probably damaging |
Het |
| V1ra8 |
T |
A |
6: 90,180,295 (GRCm39) |
I166K |
probably damaging |
Het |
| Vmn1r56 |
A |
G |
7: 5,199,575 (GRCm39) |
V14A |
probably benign |
Het |
| Vsig8 |
T |
C |
1: 172,387,925 (GRCm39) |
V5A |
possibly damaging |
Het |
| Vwa8 |
A |
T |
14: 79,184,653 (GRCm39) |
S384C |
possibly damaging |
Het |
| Wwc1 |
C |
T |
11: 35,744,264 (GRCm39) |
E853K |
probably benign |
Het |
| Zfp984 |
T |
C |
4: 147,840,381 (GRCm39) |
N157D |
probably benign |
Het |
| Zzef1 |
G |
A |
11: 72,765,816 (GRCm39) |
D1448N |
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 |
|
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'- AGCTTTTGACTACAAAGCACG -3'
(R):5'- GCCAAATTTTCTCCAATGTATTGCTTG -3'
Sequencing Primer
(F):5'- GCTTCAGCTTCCAGAGTACTGAG -3'
(R):5'- GAGACTGTCTATGGAACTCCTGC -3'
|
| Posted On |
2018-06-06 |
Incidental Mutation