Incidental Mutation 'R1301:Sycp1'
| ID |
158350 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp1
|
| Ensembl Gene |
ENSMUSG00000027855 |
| Gene Name |
synaptonemal complex protein 1 |
| Synonyms |
SCP1 |
| MMRRC Submission |
039367-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.495)
|
| Stock # |
R1301 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
102725815-102843416 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 102827938 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 270
(I270V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000143651
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000196988]
[ENSMUST00000199930]
|
| AlphaFold |
Q62209 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029448
AA Change: I270V
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: I270V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000196988
AA Change: I270V
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: I270V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000199930
|
| SMART Domains |
Protein: ENSMUSP00000143493
Gene: ENSMUSG00000027855
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
95 |
2e-33 |
PFAM |
|
Pfam:SCP-1
|
93 |
182 |
9.8e-53 |
PFAM |
|
| Meta Mutation Damage Score |
0.0774 |
| Coding Region Coverage |
- 1x: 98.7%
- 3x: 97.5%
- 10x: 93.3%
- 20x: 82.6%
|
| Validation Efficiency |
96% (67/70) |
| 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: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl4fm2 |
T |
A |
4: 144,291,635 (GRCm39) |
I24L |
probably benign |
Het |
| Ano1 |
A |
G |
7: 144,187,426 (GRCm39) |
W447R |
possibly damaging |
Het |
| Blm |
T |
A |
7: 80,105,165 (GRCm39) |
K103* |
probably null |
Het |
| Camta2 |
A |
G |
11: 70,567,230 (GRCm39) |
I675T |
probably benign |
Het |
| Catsperz |
G |
A |
19: 6,902,450 (GRCm39) |
R15C |
probably damaging |
Het |
| Chd1l |
T |
C |
3: 97,510,964 (GRCm39) |
|
probably benign |
Het |
| Corin |
C |
A |
5: 72,462,276 (GRCm39) |
E844D |
possibly damaging |
Het |
| Cyb5rl |
T |
G |
4: 106,938,104 (GRCm39) |
M127R |
probably damaging |
Het |
| Dcdc2a |
A |
T |
13: 25,286,569 (GRCm39) |
N164I |
possibly damaging |
Het |
| Dnah6 |
A |
G |
6: 73,185,528 (GRCm39) |
|
probably null |
Het |
| Emilin2 |
T |
C |
17: 71,562,960 (GRCm39) |
|
probably benign |
Het |
| Epb41l2 |
T |
A |
10: 25,319,800 (GRCm39) |
V211D |
probably damaging |
Het |
| Fbxo47 |
C |
T |
11: 97,759,427 (GRCm39) |
M166I |
probably benign |
Het |
| Golm1 |
T |
C |
13: 59,786,187 (GRCm39) |
D335G |
probably damaging |
Het |
| Gpn1 |
T |
A |
5: 31,660,773 (GRCm39) |
M188K |
probably damaging |
Het |
| Gpr84 |
T |
A |
15: 103,217,646 (GRCm39) |
S144C |
probably damaging |
Het |
| Grm8 |
G |
T |
6: 27,981,200 (GRCm39) |
Q237K |
possibly damaging |
Het |
| Gsdmd |
C |
A |
15: 75,738,908 (GRCm39) |
|
probably null |
Het |
| Hmgcr |
G |
A |
13: 96,795,528 (GRCm39) |
T347I |
probably damaging |
Het |
| Hsd17b7 |
T |
A |
1: 169,788,774 (GRCm39) |
|
probably benign |
Het |
| Hsd3b9 |
G |
A |
3: 98,354,182 (GRCm39) |
Q106* |
probably null |
Het |
| Klhl7 |
T |
G |
5: 24,364,489 (GRCm39) |
W508G |
probably damaging |
Het |
| Lrp2 |
C |
A |
2: 69,258,948 (GRCm39) |
D4581Y |
probably damaging |
Het |
| Lrrc7 |
T |
C |
3: 157,840,968 (GRCm39) |
N1357D |
probably benign |
Het |
| Macf1 |
T |
C |
4: 123,380,451 (GRCm39) |
|
probably benign |
Het |
| Mroh7 |
T |
C |
4: 106,577,692 (GRCm39) |
T329A |
probably damaging |
Het |
| Mroh9 |
C |
T |
1: 162,871,552 (GRCm39) |
|
probably null |
Het |
| Mta2 |
A |
G |
19: 8,926,550 (GRCm39) |
|
probably benign |
Het |
| Myo3a |
A |
T |
2: 22,271,906 (GRCm39) |
|
probably benign |
Het |
| Nrip2 |
A |
G |
6: 128,384,352 (GRCm39) |
D153G |
probably benign |
Het |
| Nup133 |
T |
C |
8: 124,644,156 (GRCm39) |
|
probably benign |
Het |
| Nup210 |
C |
T |
6: 91,019,329 (GRCm39) |
V259M |
possibly damaging |
Het |
| Or10ak14 |
C |
T |
4: 118,610,816 (GRCm39) |
M308I |
probably benign |
Het |
| Or5b112 |
A |
T |
19: 13,319,211 (GRCm39) |
I30F |
probably benign |
Het |
| Or9i14 |
A |
T |
19: 13,792,726 (GRCm39) |
V76D |
probably damaging |
Het |
| Otog |
C |
T |
7: 45,939,113 (GRCm39) |
R2048C |
probably damaging |
Het |
| Pacc1 |
T |
C |
1: 191,080,632 (GRCm39) |
V284A |
probably damaging |
Het |
| Paqr7 |
T |
C |
4: 134,235,124 (GRCm39) |
L327P |
probably damaging |
Het |
| Parl |
A |
G |
16: 20,105,676 (GRCm39) |
S249P |
probably damaging |
Het |
| Phc1 |
A |
G |
6: 122,302,833 (GRCm39) |
I230T |
probably benign |
Het |
| Pitpnm1 |
T |
G |
19: 4,160,831 (GRCm39) |
|
probably null |
Het |
| Plpp1 |
A |
G |
13: 112,971,477 (GRCm39) |
Y48C |
probably damaging |
Het |
| Pxdc1 |
A |
G |
13: 34,812,870 (GRCm39) |
F194L |
probably benign |
Het |
| Rp1 |
A |
T |
1: 4,416,159 (GRCm39) |
V1651D |
possibly damaging |
Het |
| Serpinb1c |
T |
A |
13: 33,080,943 (GRCm39) |
R47* |
probably null |
Het |
| Sis |
T |
C |
3: 72,853,915 (GRCm39) |
T521A |
possibly damaging |
Het |
| Slc16a9 |
A |
G |
10: 70,118,308 (GRCm39) |
D209G |
probably benign |
Het |
| Slc26a4 |
A |
T |
12: 31,575,567 (GRCm39) |
C706* |
probably null |
Het |
| Slc37a2 |
A |
G |
9: 37,148,177 (GRCm39) |
V325A |
probably benign |
Het |
| Speg |
T |
A |
1: 75,378,145 (GRCm39) |
D784E |
probably damaging |
Het |
| Tatdn2 |
T |
A |
6: 113,681,076 (GRCm39) |
F309I |
probably damaging |
Het |
| Tmem67 |
T |
C |
4: 12,089,400 (GRCm39) |
|
probably benign |
Het |
| Trpm1 |
T |
A |
7: 63,852,801 (GRCm39) |
|
probably null |
Het |
| Wrn |
T |
C |
8: 33,782,714 (GRCm39) |
R496G |
probably damaging |
Het |
| Zfhx2 |
A |
G |
14: 55,300,854 (GRCm39) |
V2299A |
probably benign |
Het |
| Zfp819 |
T |
A |
7: 43,266,524 (GRCm39) |
S260T |
possibly 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 |
|
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 |
|
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'- TGCCCTCCTTCAACTGATCCAAAC -3'
(R):5'- CCACGAGACTGATTTAGATGTTCCTTCC -3'
Sequencing Primer
(F):5'- TCCTTCAACTGATCCAAACAAAGTG -3'
(R):5'- CTATTACTGATGATAAGGCTCAGGTG -3'
|
| Posted On |
2014-02-18 |
Incidental Mutation