Incidental Mutation 'R2516:Sycp1'
| ID |
253759 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp1
|
| Ensembl Gene |
ENSMUSG00000027855 |
| Gene Name |
synaptonemal complex protein 1 |
| Synonyms |
SCP1 |
| MMRRC Submission |
040420-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.539)
|
| Stock # |
R2516 (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 102752382 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 800
(E800G)
|
| 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: E800G
PolyPhen 2
Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: E800G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000196988
AA Change: E800G
PolyPhen 2
Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: E800G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Meta Mutation Damage Score |
0.0804 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.1%
|
| Validation Efficiency |
98% (65/66) |
| 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: 66 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb11 |
A |
T |
2: 69,159,673 (GRCm39) |
I6N |
possibly damaging |
Het |
| Aen |
T |
C |
7: 78,555,616 (GRCm39) |
V188A |
probably damaging |
Het |
| Afg3l1 |
A |
G |
8: 124,228,693 (GRCm39) |
E753G |
probably damaging |
Het |
| Alas1 |
G |
A |
9: 106,115,859 (GRCm39) |
T385I |
probably damaging |
Het |
| Alms1 |
C |
A |
6: 85,644,945 (GRCm39) |
|
probably benign |
Het |
| Ankrd65 |
A |
G |
4: 155,875,868 (GRCm39) |
T30A |
possibly damaging |
Het |
| App |
T |
C |
16: 84,775,117 (GRCm39) |
S582G |
probably damaging |
Het |
| Arfgef1 |
A |
T |
1: 10,223,879 (GRCm39) |
V1473E |
possibly damaging |
Het |
| Arhgap21 |
G |
A |
2: 20,859,809 (GRCm39) |
P1196S |
probably damaging |
Het |
| Arhgap24 |
A |
G |
5: 103,039,776 (GRCm39) |
T238A |
probably benign |
Het |
| Atf7 |
T |
C |
15: 102,437,439 (GRCm39) |
|
probably benign |
Het |
| Best1 |
G |
T |
19: 9,970,675 (GRCm39) |
S55* |
probably null |
Het |
| Capn11 |
A |
G |
17: 45,944,725 (GRCm39) |
V514A |
probably damaging |
Het |
| Cep104 |
T |
A |
4: 154,073,603 (GRCm39) |
M52K |
probably damaging |
Het |
| Clca3a1 |
C |
T |
3: 144,443,619 (GRCm39) |
|
probably null |
Het |
| Cyp3a25 |
T |
C |
5: 145,939,837 (GRCm39) |
|
probably null |
Het |
| Dmxl2 |
G |
A |
9: 54,307,378 (GRCm39) |
P2197S |
probably damaging |
Het |
| Drosha |
T |
C |
15: 12,859,551 (GRCm39) |
|
probably null |
Het |
| Exosc9 |
A |
G |
3: 36,617,311 (GRCm39) |
K355R |
probably benign |
Het |
| Fut1 |
A |
C |
7: 45,268,622 (GRCm39) |
H192P |
probably benign |
Het |
| Gm572 |
T |
A |
4: 148,748,841 (GRCm39) |
V166D |
possibly damaging |
Het |
| Gm9966 |
C |
T |
7: 95,607,735 (GRCm39) |
P19S |
unknown |
Het |
| Gmds |
C |
T |
13: 32,284,456 (GRCm39) |
V219I |
probably damaging |
Het |
| Gsn |
G |
A |
2: 35,173,965 (GRCm39) |
E25K |
probably benign |
Het |
| Il4i1 |
T |
C |
7: 44,489,315 (GRCm39) |
F368S |
probably damaging |
Het |
| Irak1bp1 |
T |
C |
9: 82,712,373 (GRCm39) |
L98P |
probably damaging |
Het |
| Khdrbs3 |
T |
C |
15: 68,896,544 (GRCm39) |
|
probably benign |
Het |
| Kndc1 |
T |
C |
7: 139,501,738 (GRCm39) |
I925T |
probably damaging |
Het |
| Laptm4a |
T |
C |
12: 8,988,151 (GRCm39) |
I296T |
probably benign |
Het |
| Lpl |
A |
T |
8: 69,340,170 (GRCm39) |
H55L |
probably benign |
Het |
| Lrrk2 |
C |
A |
15: 91,640,130 (GRCm39) |
N1558K |
probably benign |
Het |
| Mfsd2a |
A |
G |
4: 122,844,280 (GRCm39) |
L289P |
probably damaging |
Het |
| Mmrn2 |
T |
A |
14: 34,120,759 (GRCm39) |
M543K |
probably benign |
Het |
| Mnat1 |
T |
C |
12: 73,228,550 (GRCm39) |
|
probably benign |
Het |
| Msto1 |
A |
T |
3: 88,819,200 (GRCm39) |
|
probably null |
Het |
| Mtus1 |
A |
G |
8: 41,535,776 (GRCm39) |
Y647H |
probably damaging |
Het |
| Nars1 |
A |
T |
18: 64,638,087 (GRCm39) |
V289E |
probably damaging |
Het |
| Oit3 |
T |
A |
10: 59,264,167 (GRCm39) |
K322N |
probably damaging |
Het |
| Oit3 |
G |
A |
10: 59,277,507 (GRCm39) |
|
probably benign |
Het |
| Or4k1 |
T |
C |
14: 50,377,440 (GRCm39) |
I219V |
probably benign |
Het |
| Or5b113 |
T |
A |
19: 13,342,557 (GRCm39) |
C188* |
probably null |
Het |
| Or5m12 |
A |
G |
2: 85,734,900 (GRCm39) |
I166T |
probably benign |
Het |
| Or6c211 |
G |
A |
10: 129,506,155 (GRCm39) |
R78W |
probably damaging |
Het |
| Pecr |
A |
T |
1: 72,316,469 (GRCm39) |
C79S |
probably damaging |
Het |
| Plekhn1 |
T |
C |
4: 156,307,116 (GRCm39) |
D478G |
probably damaging |
Het |
| Pls1 |
A |
T |
9: 95,658,616 (GRCm39) |
M264K |
probably benign |
Het |
| Ptprj |
C |
A |
2: 90,305,340 (GRCm39) |
|
probably benign |
Het |
| Pygm |
A |
G |
19: 6,447,631 (GRCm39) |
D646G |
probably benign |
Het |
| Rif1 |
GCCACCA |
GCCA |
2: 52,000,336 (GRCm39) |
|
probably benign |
Het |
| Scn8a |
T |
C |
15: 100,867,043 (GRCm39) |
V283A |
probably benign |
Het |
| Shisa5 |
T |
C |
9: 108,885,575 (GRCm39) |
|
probably null |
Het |
| Slc10a4 |
A |
G |
5: 73,165,848 (GRCm39) |
I246V |
possibly damaging |
Het |
| Slc1a1 |
A |
T |
19: 28,870,312 (GRCm39) |
I104F |
probably benign |
Het |
| Slc22a8 |
A |
G |
19: 8,587,559 (GRCm39) |
Y511C |
probably benign |
Het |
| Slc6a5 |
A |
G |
7: 49,606,210 (GRCm39) |
N706S |
probably benign |
Het |
| Sos2 |
T |
C |
12: 69,697,433 (GRCm39) |
K96E |
probably damaging |
Het |
| Stom |
G |
A |
2: 35,205,977 (GRCm39) |
R251* |
probably null |
Het |
| Tab2 |
G |
A |
10: 7,783,245 (GRCm39) |
P679L |
probably damaging |
Het |
| Tiam2 |
G |
A |
17: 3,503,657 (GRCm39) |
V945I |
probably damaging |
Het |
| Trpm5 |
G |
T |
7: 142,628,254 (GRCm39) |
P1007Q |
probably damaging |
Het |
| Uchl1 |
T |
G |
5: 66,839,956 (GRCm39) |
I139S |
probably damaging |
Het |
| Vmn1r232 |
A |
G |
17: 21,134,288 (GRCm39) |
I104T |
possibly damaging |
Het |
| Vmn2r97 |
G |
A |
17: 19,167,814 (GRCm39) |
M689I |
probably benign |
Het |
| Zc3h18 |
A |
T |
8: 123,129,904 (GRCm39) |
|
probably benign |
Het |
| Zfhx4 |
C |
T |
3: 5,468,418 (GRCm39) |
P2859S |
probably benign |
Het |
| Zfp456 |
T |
C |
13: 67,510,491 (GRCm39) |
K99R |
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 |
|
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'- AGTTATGAGCAACAAGAACTATTTCT -3'
(R):5'- TGTCTGTAACTGTTACTCTGTAGTT -3'
Sequencing Primer
(F):5'- TAAGGGCTTAGGTCCAAC -3'
(R):5'- CACTAGTTATTTCACAGAGGTA -3'
|
| Posted On |
2014-12-04 |
Incidental Mutation