Incidental Mutation 'R2858:Sycp3'
| ID |
252580 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sycp3
|
| Ensembl Gene |
ENSMUSG00000020059 |
| Gene Name |
synaptonemal complex protein 3 |
| Synonyms |
Scp3, Cor1 |
| MMRRC Submission |
040448-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.127)
|
| Stock # |
R2858 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
88295449-88309098 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 88303234 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 166
(E166G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000137800
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000020252]
[ENSMUST00000117440]
[ENSMUST00000123244]
[ENSMUST00000125612]
[ENSMUST00000148899]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000020252
AA Change: E166G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000020252
Gene: ENSMUSG00000020059
AA Change: E166G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
42 |
53 |
N/A |
INTRINSIC |
|
Pfam:Cor1
|
101 |
229 |
6.1e-57 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000117440
|
| SMART Domains |
Protein: ENSMUSP00000112708
Gene: ENSMUSG00000060002
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
12 |
N/A |
INTRINSIC |
|
Pfam:CDP-OH_P_transf
|
61 |
136 |
8.8e-18 |
PFAM |
|
transmembrane domain
|
159 |
181 |
N/A |
INTRINSIC |
|
transmembrane domain
|
191 |
213 |
N/A |
INTRINSIC |
|
transmembrane domain
|
226 |
248 |
N/A |
INTRINSIC |
|
transmembrane domain
|
263 |
282 |
N/A |
INTRINSIC |
|
transmembrane domain
|
295 |
317 |
N/A |
INTRINSIC |
|
transmembrane domain
|
349 |
371 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000123244
|
| SMART Domains |
Protein: ENSMUSP00000137704
Gene: ENSMUSG00000020059
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
42 |
53 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000125612
AA Change: E166G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000137800
Gene: ENSMUSG00000020059
AA Change: E166G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
42 |
53 |
N/A |
INTRINSIC |
|
Pfam:Cor1
|
100 |
229 |
7.6e-60 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000134318
|
| SMART Domains |
Protein: ENSMUSP00000122428
Gene: ENSMUSG00000060002
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
20 |
42 |
N/A |
INTRINSIC |
|
transmembrane domain
|
55 |
77 |
N/A |
INTRINSIC |
|
transmembrane domain
|
109 |
131 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148899
|
| SMART Domains |
Protein: ENSMUSP00000120167
Gene: ENSMUSG00000060002
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
25 |
47 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.6416 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.2%
|
| Validation Efficiency |
100% (37/37) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an essential structural component of the synaptonemal complex. This complex is involved in synapsis, recombination and segregation of meiotic chromosomes. Mutations in this gene are associated with azoospermia in males and susceptibility to pregnancy loss in females. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2010]
PHENOTYPE: Homozygous mutants are male infertile and female sub-fertile. Reduced litter size in females is due to achiasmatic oocytes, resulting in aneuploidy and embryonic death. Meiosis in males blocks at early prophase with lack of synaptonemal complexes. [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 |
|---|
| 1700028K03Rik |
T |
A |
5: 107,693,667 (GRCm39) |
F95I |
probably benign |
Het |
| Abcg5 |
A |
G |
17: 84,977,648 (GRCm39) |
|
probably null |
Het |
| Amfr |
A |
T |
8: 94,731,842 (GRCm39) |
N11K |
probably damaging |
Het |
| Bltp3a |
G |
T |
17: 28,104,436 (GRCm39) |
R494L |
probably damaging |
Het |
| Cd109 |
CATTTATTTATTTATTTATTTATTTATTTATTTAT |
CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT |
9: 78,619,782 (GRCm39) |
|
probably benign |
Het |
| Cdh23 |
C |
T |
10: 60,218,432 (GRCm39) |
|
probably null |
Het |
| Chd4 |
A |
G |
6: 125,081,849 (GRCm39) |
K481R |
probably damaging |
Het |
| Cyp2a22 |
T |
C |
7: 26,633,687 (GRCm39) |
Y341C |
probably damaging |
Het |
| Ddb2 |
T |
C |
2: 91,047,022 (GRCm39) |
T338A |
probably damaging |
Het |
| Fat2 |
A |
G |
11: 55,174,599 (GRCm39) |
V2038A |
possibly damaging |
Het |
| Fbxo36 |
A |
G |
1: 84,874,316 (GRCm39) |
K104R |
probably benign |
Het |
| Fmo9 |
A |
C |
1: 166,501,236 (GRCm39) |
F237C |
probably damaging |
Het |
| Helz |
G |
A |
11: 107,563,753 (GRCm39) |
|
probably benign |
Het |
| Hivep2 |
C |
A |
10: 14,004,713 (GRCm39) |
T437K |
probably benign |
Het |
| Ifit1bl1 |
A |
T |
19: 34,571,722 (GRCm39) |
I245K |
probably benign |
Het |
| Ighv1-22 |
T |
C |
12: 114,709,918 (GRCm39) |
D109G |
probably damaging |
Het |
| Kcnk10 |
T |
C |
12: 98,401,548 (GRCm39) |
R376G |
possibly damaging |
Het |
| Lrrc66 |
T |
A |
5: 73,764,646 (GRCm39) |
E799V |
probably benign |
Het |
| Lrrc7 |
T |
A |
3: 157,867,362 (GRCm39) |
N793I |
probably damaging |
Het |
| Nexn |
C |
T |
3: 151,953,680 (GRCm39) |
E247K |
probably damaging |
Het |
| Ntmt1 |
A |
G |
2: 30,712,377 (GRCm39) |
H140R |
probably damaging |
Het |
| Or11g27 |
T |
A |
14: 50,770,897 (GRCm39) |
N9K |
probably benign |
Het |
| Or3a10 |
C |
T |
11: 73,935,653 (GRCm39) |
G149D |
possibly damaging |
Het |
| Or9e1 |
T |
A |
11: 58,732,708 (GRCm39) |
V256E |
probably benign |
Het |
| Pask |
A |
G |
1: 93,249,373 (GRCm39) |
Y676H |
probably benign |
Het |
| Polq |
T |
A |
16: 36,883,115 (GRCm39) |
F1760I |
possibly damaging |
Het |
| Ppp1r1b |
T |
C |
11: 98,246,145 (GRCm39) |
|
probably benign |
Het |
| Psmf1 |
A |
G |
2: 151,571,456 (GRCm39) |
L169P |
probably damaging |
Het |
| Rcbtb1 |
T |
A |
14: 59,458,861 (GRCm39) |
|
probably null |
Het |
| S1pr4 |
C |
A |
10: 81,335,073 (GRCm39) |
A134S |
probably damaging |
Het |
| Setx |
GTGGCT |
GT |
2: 29,044,073 (GRCm39) |
1814 |
probably null |
Het |
| Slc24a1 |
T |
C |
9: 64,856,614 (GRCm39) |
I98V |
unknown |
Het |
| Slc6a21 |
G |
A |
7: 44,929,952 (GRCm39) |
A147T |
possibly damaging |
Het |
| Vmn2r82 |
T |
A |
10: 79,217,090 (GRCm39) |
I474N |
probably damaging |
Het |
| Zfp1007 |
T |
C |
5: 109,823,819 (GRCm39) |
T544A |
probably benign |
Het |
|
| Other mutations in Sycp3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02103:Sycp3
|
APN |
10 |
88,302,334 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
IGL02402:Sycp3
|
APN |
10 |
88,302,425 (GRCm39) |
intron |
probably benign |
|
|
PIT4378001:Sycp3
|
UTSW |
10 |
88,302,366 (GRCm39) |
nonsense |
probably null |
|
|
R1468:Sycp3
|
UTSW |
10 |
88,305,454 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R1468:Sycp3
|
UTSW |
10 |
88,305,454 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R2857:Sycp3
|
UTSW |
10 |
88,303,234 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2897:Sycp3
|
UTSW |
10 |
88,308,544 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R2898:Sycp3
|
UTSW |
10 |
88,308,544 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R4194:Sycp3
|
UTSW |
10 |
88,299,237 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5683:Sycp3
|
UTSW |
10 |
88,308,797 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6882:Sycp3
|
UTSW |
10 |
88,308,791 (GRCm39) |
nonsense |
probably null |
|
|
R7273:Sycp3
|
UTSW |
10 |
88,305,428 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7853:Sycp3
|
UTSW |
10 |
88,302,368 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8055:Sycp3
|
UTSW |
10 |
88,298,438 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8147:Sycp3
|
UTSW |
10 |
88,298,467 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8720:Sycp3
|
UTSW |
10 |
88,298,394 (GRCm39) |
missense |
probably benign |
0.38 |
|
R8872:Sycp3
|
UTSW |
10 |
88,302,388 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9163:Sycp3
|
UTSW |
10 |
88,299,734 (GRCm39) |
critical splice donor site |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- AGCATGTGAGAAGACATCTGTTAAG -3'
(R):5'- ATACTTCTGGGGTTTACCATTTGGC -3'
Sequencing Primer
(F):5'- GAAATTTGACAGGATTCACTGT -3'
(R):5'- TGGCAATATTAAAACATGTACCTGAC -3'
|
| Posted On |
2014-12-04 |
Incidental Mutation