Incidental Mutation 'R5477:Sycp1'
| ID |
434109 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp1
|
| Ensembl Gene |
ENSMUSG00000027855 |
| Gene Name |
synaptonemal complex protein 1 |
| Synonyms |
SCP1 |
| MMRRC Submission |
043038-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.495)
|
| Stock # |
R5477 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 102726206 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tryptophan to Arginine
at position 973
(W973R)
|
| 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: W973R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: W973R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000196988
AA Change: W973R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: W973R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000198651
|
| Coding Region Coverage |
- 1x: 98.3%
- 3x: 97.3%
- 10x: 95.3%
- 20x: 90.9%
|
| 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: 34 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930505A04Rik |
C |
T |
11: 30,376,349 (GRCm39) |
V173M |
probably damaging |
Het |
| Aacs |
T |
C |
5: 125,588,984 (GRCm39) |
Y421H |
probably damaging |
Het |
| Abca13 |
A |
G |
11: 9,251,298 (GRCm39) |
K2890R |
possibly damaging |
Het |
| Aff4 |
T |
A |
11: 53,299,299 (GRCm39) |
|
probably null |
Het |
| Brd10 |
A |
G |
19: 29,731,518 (GRCm39) |
V498A |
probably benign |
Het |
| Cntn4 |
A |
T |
6: 106,650,911 (GRCm39) |
Q698L |
possibly damaging |
Het |
| D5Ertd579e |
G |
T |
5: 36,772,601 (GRCm39) |
S598Y |
probably damaging |
Het |
| Dmrt1 |
A |
G |
19: 25,487,164 (GRCm39) |
M157V |
probably benign |
Het |
| Dnah2 |
C |
T |
11: 69,349,746 (GRCm39) |
R2399Q |
probably benign |
Het |
| Gm10521 |
T |
A |
1: 171,724,067 (GRCm39) |
M126K |
unknown |
Het |
| Hs2st1 |
A |
G |
3: 144,262,709 (GRCm39) |
|
probably benign |
Het |
| Lats2 |
T |
C |
14: 57,937,010 (GRCm39) |
D113G |
probably benign |
Het |
| Myo15a |
A |
C |
11: 60,368,503 (GRCm39) |
D421A |
probably damaging |
Het |
| Or5k15 |
T |
A |
16: 58,710,107 (GRCm39) |
I159F |
probably benign |
Het |
| Or5k17 |
A |
T |
16: 58,746,393 (GRCm39) |
D180E |
possibly damaging |
Het |
| Or6z6 |
T |
C |
7: 6,491,570 (GRCm39) |
Y94C |
probably benign |
Het |
| Pappa2 |
T |
A |
1: 158,784,308 (GRCm39) |
D234V |
probably benign |
Het |
| Parl |
G |
T |
16: 20,098,824 (GRCm39) |
T311K |
possibly damaging |
Het |
| Pias3 |
G |
A |
3: 96,612,319 (GRCm39) |
R557H |
probably damaging |
Het |
| Pskh1 |
C |
T |
8: 106,656,511 (GRCm39) |
R396C |
probably damaging |
Het |
| Rc3h2 |
T |
C |
2: 37,289,642 (GRCm39) |
D390G |
possibly damaging |
Het |
| Ryr2 |
G |
T |
13: 11,720,542 (GRCm39) |
P2702Q |
probably damaging |
Het |
| Senp6 |
C |
A |
9: 80,051,125 (GRCm39) |
A961D |
probably damaging |
Het |
| Slc27a3 |
A |
G |
3: 90,294,146 (GRCm39) |
S503P |
probably benign |
Het |
| Slc39a12 |
T |
C |
2: 14,394,193 (GRCm39) |
V21A |
possibly damaging |
Het |
| Sox7 |
A |
G |
14: 64,185,945 (GRCm39) |
Y327C |
probably damaging |
Het |
| Spdl1 |
A |
T |
11: 34,713,037 (GRCm39) |
F288I |
possibly damaging |
Het |
| Ssbp2 |
T |
A |
13: 91,812,244 (GRCm39) |
M127K |
probably damaging |
Het |
| Sspo |
A |
C |
6: 48,475,327 (GRCm39) |
S5032R |
possibly damaging |
Het |
| Tm4sf5 |
C |
T |
11: 70,401,174 (GRCm39) |
T130I |
probably benign |
Het |
| Top2a |
T |
A |
11: 98,907,306 (GRCm39) |
K175* |
probably null |
Het |
| Trim30d |
T |
A |
7: 104,121,347 (GRCm39) |
Y316F |
probably damaging |
Het |
| Vmn1r124 |
G |
A |
7: 20,993,653 (GRCm39) |
P297L |
probably damaging |
Het |
| Zfp715 |
T |
C |
7: 42,949,378 (GRCm39) |
Y194C |
probably 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 |
|
|
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'- TGATTAACTATTCAGAGACCCTCAC -3'
(R):5'- GCCTGGTTTCAGAGGAAGATG -3'
Sequencing Primer
(F):5'- CTTCGAACTTCAATATCCATTGCAAG -3'
(R):5'- TGGTTTCAGAGGAAGATGTATCAAAC -3'
|
| Posted On |
2016-10-06 |
Incidental Mutation