Incidental Mutation 'PIT4458001:Sycp1'
| ID |
555901 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp1
|
| Ensembl Gene |
ENSMUSG00000027855 |
| Gene Name |
synaptonemal complex protein 1 |
| Synonyms |
SCP1 |
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.539)
|
| Stock # |
PIT4458001 (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 T
at 102842149 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 53
(S53T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000029448
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029448]
[ENSMUST00000058899]
[ENSMUST00000196988]
[ENSMUST00000199930]
|
| AlphaFold |
Q62209 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029448
AA Change: S53T
PolyPhen 2
Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: S53T
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000058899
|
| SMART Domains |
Protein: ENSMUSP00000052557
Gene: ENSMUSG00000048938
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:HOLI
|
2 |
47 |
5e-9 |
BLAST |
|
ZnF_C4
|
119 |
190 |
2.51e-36 |
SMART |
|
HOLI
|
289 |
474 |
1.74e-21 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000196988
AA Change: S53T
PolyPhen 2
Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: S53T
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
809 |
N/A |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000199930
AA Change: S53T
PolyPhen 2
Score 0.317 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000143493
Gene: ENSMUSG00000027855
AA Change: S53T
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SCP-1
|
28 |
95 |
2e-33 |
PFAM |
|
Pfam:SCP-1
|
93 |
182 |
9.8e-53 |
PFAM |
|
| Coding Region Coverage |
- 1x: 93.1%
- 3x: 90.8%
- 10x: 85.3%
- 20x: 73.0%
|
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca13 |
G |
T |
11: 9,248,304 (GRCm39) |
V2684L |
probably benign |
Het |
| Adamts9 |
T |
A |
6: 92,866,886 (GRCm39) |
I718F |
probably damaging |
Het |
| Adcyap1r1 |
A |
G |
6: 55,455,067 (GRCm39) |
D110G |
probably benign |
Het |
| Adgrd1 |
G |
A |
5: 129,208,641 (GRCm39) |
G281D |
probably damaging |
Het |
| Afg1l |
A |
T |
10: 42,330,366 (GRCm39) |
C100* |
probably null |
Het |
| Atp2a2 |
G |
A |
5: 122,595,372 (GRCm39) |
Q993* |
probably null |
Het |
| Baz1a |
A |
G |
12: 54,977,095 (GRCm39) |
M389T |
probably benign |
Het |
| Btnl4 |
T |
A |
17: 34,693,242 (GRCm39) |
M58L |
probably benign |
Het |
| Card6 |
TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG |
TTGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGTGGATGAGAGGGCTTAGCATGGGAGGACTGCGGATGAGAGGGCTTAGCATGGGAGGACTG |
15: 5,128,173 (GRCm39) |
|
probably benign |
Het |
| Cpeb1 |
A |
T |
7: 80,998,180 (GRCm39) |
F533Y |
probably damaging |
Het |
| Ctnna1 |
T |
A |
18: 35,308,179 (GRCm39) |
N166K |
possibly damaging |
Het |
| Ecsit |
T |
C |
9: 21,987,580 (GRCm39) |
H153R |
probably damaging |
Het |
| Gbp8 |
T |
C |
5: 105,162,955 (GRCm39) |
K480E |
probably benign |
Het |
| Glyat |
A |
T |
19: 12,625,373 (GRCm39) |
T66S |
probably benign |
Het |
| Gm1110 |
T |
C |
9: 26,792,124 (GRCm39) |
Q632R |
probably benign |
Het |
| Gm12185 |
C |
T |
11: 48,798,738 (GRCm39) |
R585Q |
probably damaging |
Het |
| Gm17669 |
TAA |
TAAA |
18: 67,695,819 (GRCm39) |
|
probably null |
Het |
| Gm7489 |
A |
C |
15: 53,749,195 (GRCm39) |
E89A |
unknown |
Het |
| Grb7 |
C |
T |
11: 98,344,655 (GRCm39) |
Q353* |
probably null |
Het |
| Ifi207 |
G |
A |
1: 173,562,738 (GRCm39) |
T136I |
unknown |
Het |
| Ighv3-1 |
T |
C |
12: 113,928,224 (GRCm39) |
Y45C |
probably benign |
Het |
| Ing5 |
A |
G |
1: 93,739,668 (GRCm39) |
M92V |
possibly damaging |
Het |
| Ivl |
TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG |
TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG |
3: 92,479,608 (GRCm39) |
|
probably benign |
Het |
| Kdm6b |
A |
T |
11: 69,290,778 (GRCm39) |
D1630E |
unknown |
Het |
| Lmo7 |
C |
T |
14: 102,124,923 (GRCm39) |
Q583* |
probably null |
Het |
| Lrrc37a |
T |
C |
11: 103,395,338 (GRCm39) |
D29G |
probably benign |
Het |
| Mpdz |
G |
T |
4: 81,337,263 (GRCm39) |
A10D |
probably damaging |
Het |
| Myh4 |
A |
G |
11: 67,131,821 (GRCm39) |
M94V |
possibly damaging |
Het |
| Nectin2 |
A |
C |
7: 19,472,252 (GRCm39) |
L46V |
probably benign |
Het |
| Nynrin |
A |
T |
14: 56,101,425 (GRCm39) |
T365S |
probably benign |
Het |
| Or4c120 |
A |
T |
2: 89,000,977 (GRCm39) |
I193K |
probably benign |
Het |
| Pde4b |
A |
C |
4: 102,459,875 (GRCm39) |
E570A |
probably damaging |
Het |
| Phf3 |
T |
C |
1: 30,855,622 (GRCm39) |
H988R |
probably damaging |
Het |
| Ppfia2 |
A |
G |
10: 106,763,708 (GRCm39) |
K1234E |
probably benign |
Het |
| Prl7c1 |
A |
T |
13: 27,957,741 (GRCm39) |
M233K |
probably benign |
Het |
| Prp2 |
C |
T |
6: 132,577,510 (GRCm39) |
P266S |
unknown |
Het |
| Ralgds |
T |
C |
2: 28,432,486 (GRCm39) |
L160P |
probably damaging |
Het |
| Rasa1 |
A |
T |
13: 85,375,237 (GRCm39) |
M664K |
possibly damaging |
Het |
| Ryr2 |
T |
C |
13: 11,570,334 (GRCm39) |
T4930A |
probably benign |
Het |
| Senp8 |
T |
C |
9: 59,644,763 (GRCm39) |
Y131C |
probably damaging |
Het |
| Sp100 |
A |
G |
1: 85,635,837 (GRCm39) |
I547M |
probably benign |
Het |
| Spata20 |
A |
G |
11: 94,375,434 (GRCm39) |
M120T |
probably damaging |
Het |
| Spata31 |
A |
G |
13: 65,069,664 (GRCm39) |
H604R |
probably benign |
Het |
| Tgm1 |
T |
C |
14: 55,950,022 (GRCm39) |
D62G |
unknown |
Het |
| Trpm1 |
G |
C |
7: 63,918,309 (GRCm39) |
E1434Q |
possibly damaging |
Het |
| Tshb |
A |
T |
3: 102,685,480 (GRCm39) |
Y50N |
probably damaging |
Het |
| Wdr17 |
A |
T |
8: 55,126,614 (GRCm39) |
Y413* |
probably null |
Het |
| Zdhhc16 |
G |
A |
19: 41,926,209 (GRCm39) |
G55R |
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 |
|
|
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 |
|
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'- TGTTCGAGCATGGGCAAAATAC -3'
(R):5'- CTGCTATAGCTAAGACATGTCATTG -3'
Sequencing Primer
(F):5'- AGTTTTTGAAAAGCAGGATCTGTG -3'
(R):5'- TTTGGTTGAGTGAGATTGAAGGAAAC -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation