Incidental Mutation 'R5036:Sycp1'
| ID |
389529 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp1
|
| Ensembl Gene |
ENSMUSG00000027855 |
| Gene Name |
synaptonemal complex protein 1 |
| Synonyms |
SCP1 |
| MMRRC Submission |
042627-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.539)
|
| Stock # |
R5036 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 102727916 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Methionine
at position 899
(K899M)
|
| 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: K899M
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: K899M
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000196988
AA Change: K899M
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: K899M
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000198651
|
| Meta Mutation Damage Score |
0.0915 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.2%
- 10x: 95.7%
- 20x: 90.1%
|
| Validation Efficiency |
100% (44/44) |
| 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: 35 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2610021A01Rik |
G |
A |
7: 41,275,578 (GRCm39) |
G427D |
possibly damaging |
Het |
| Agbl5 |
G |
A |
5: 31,060,403 (GRCm39) |
R141Q |
probably damaging |
Het |
| C4b |
T |
A |
17: 34,959,419 (GRCm39) |
|
probably null |
Het |
| Cabyr |
A |
T |
18: 12,884,303 (GRCm39) |
E263D |
probably damaging |
Het |
| Car1 |
A |
T |
3: 14,841,299 (GRCm39) |
D45E |
possibly damaging |
Het |
| Col25a1 |
T |
C |
3: 130,376,978 (GRCm39) |
|
probably null |
Het |
| Dnah6 |
G |
T |
6: 73,021,674 (GRCm39) |
S3549R |
probably benign |
Het |
| Dync1h1 |
A |
T |
12: 110,596,969 (GRCm39) |
I1639F |
probably damaging |
Het |
| Fhad1 |
A |
T |
4: 141,648,052 (GRCm39) |
D271E |
probably benign |
Het |
| Gle1 |
T |
C |
2: 29,826,223 (GRCm39) |
S101P |
probably benign |
Het |
| Gm4781 |
C |
A |
10: 100,232,851 (GRCm39) |
|
noncoding transcript |
Het |
| Gpatch3 |
A |
G |
4: 133,305,461 (GRCm39) |
Y232C |
probably damaging |
Het |
| Gtf2ird2 |
A |
G |
5: 134,246,349 (GRCm39) |
N869S |
probably damaging |
Het |
| Ifi204 |
G |
A |
1: 173,580,311 (GRCm39) |
P400S |
possibly damaging |
Het |
| Ighv2-2 |
T |
C |
12: 113,552,092 (GRCm39) |
T49A |
possibly damaging |
Het |
| Itsn1 |
T |
A |
16: 91,579,123 (GRCm39) |
|
probably benign |
Het |
| Mib2 |
A |
T |
4: 155,740,745 (GRCm39) |
N626K |
probably damaging |
Het |
| Nf1 |
C |
A |
11: 79,337,690 (GRCm39) |
Q1098K |
probably damaging |
Het |
| Odc1 |
C |
A |
12: 17,598,020 (GRCm39) |
Q116K |
probably damaging |
Het |
| Otof |
C |
T |
5: 30,541,783 (GRCm39) |
E761K |
possibly damaging |
Het |
| Palld |
A |
T |
8: 62,003,196 (GRCm39) |
V301D |
probably damaging |
Het |
| Pask |
A |
T |
1: 93,249,801 (GRCm39) |
L533* |
probably null |
Het |
| Plekhh2 |
T |
C |
17: 84,879,189 (GRCm39) |
S638P |
probably damaging |
Het |
| Scaf8 |
T |
A |
17: 3,214,537 (GRCm39) |
|
probably benign |
Het |
| Sdccag8 |
G |
T |
1: 176,839,541 (GRCm39) |
R695L |
probably damaging |
Het |
| Serpina1c |
A |
G |
12: 103,865,085 (GRCm39) |
I187T |
probably damaging |
Het |
| Slitrk5 |
G |
T |
14: 111,918,316 (GRCm39) |
G647W |
possibly damaging |
Het |
| Taok1 |
G |
A |
11: 77,440,157 (GRCm39) |
R617C |
probably benign |
Het |
| Tbc1d32 |
A |
C |
10: 56,071,500 (GRCm39) |
Y341* |
probably null |
Het |
| Tenm4 |
A |
G |
7: 96,343,997 (GRCm39) |
N267D |
probably damaging |
Het |
| Tenm4 |
T |
C |
7: 96,501,768 (GRCm39) |
V1287A |
probably damaging |
Het |
| Tsga10 |
A |
T |
1: 37,823,049 (GRCm39) |
V488E |
possibly damaging |
Het |
| Ttc39c |
G |
T |
18: 12,820,138 (GRCm39) |
|
probably null |
Het |
| Uck1 |
A |
T |
2: 32,148,478 (GRCm39) |
|
probably benign |
Het |
| Vmn2r98 |
A |
G |
17: 19,286,419 (GRCm39) |
I306V |
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 |
|
|
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 |
|
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'- AGAATGTTACCGTTTGTCAGTACTG -3'
(R):5'- CCAGTTTCAAATTGCCTTCAAGTG -3'
Sequencing Primer
(F):5'- GACCCTTAATAACATATTTGGCTGTG -3'
(R):5'- GCCTTCAAGTGCATGAACTAG -3'
|
| Posted On |
2016-06-06 |
Incidental Mutation