Incidental Mutation 'R8872:Sycp3'
ID 676365
Institutional Source Beutler Lab
Gene Symbol Sycp3
Ensembl Gene ENSMUSG00000020059
Gene Name synaptonemal complex protein 3
Synonyms Scp3, Cor1
MMRRC Submission 068743-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.127) question?
Stock # R8872 (G1)
Quality Score 225.009
Status Validated
Chromosome 10
Chromosomal Location 88295449-88309098 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 88302388 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Valine at position 126 (E126V)
Ref Sequence ENSEMBL: ENSMUSP00000020252 (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: E126V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000020252
Gene: ENSMUSG00000020059
AA Change: E126V

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
low complexity region 42 53 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000125612
AA Change: E126V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000137800
Gene: ENSMUSG00000020059
AA Change: E126V

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
transmembrane domain 25 47 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.5%
Validation Efficiency 99% (74/75)
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: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700067P10Rik A G 17: 48,401,164 (GRCm39) S150G possibly damaging Het
Alpk2 A T 18: 65,413,977 (GRCm39) S1579R probably damaging Het
Ank2 C T 3: 126,791,525 (GRCm39) E814K possibly damaging Het
Cep57 A G 9: 13,737,980 (GRCm39) probably benign Het
Cntnap4 A T 8: 113,585,759 (GRCm39) R1127S possibly damaging Het
Comt C A 16: 18,245,239 (GRCm39) probably benign Het
Crlf3 T C 11: 79,938,440 (GRCm39) N399S Het
Crls1 T A 2: 132,691,819 (GRCm39) S115T probably benign Het
Dixdc1 A G 9: 50,614,453 (GRCm39) S199P possibly damaging Het
Dsc3 T C 18: 20,122,679 (GRCm39) T82A probably benign Het
Efcab3 T G 11: 104,760,880 (GRCm39) L2411R probably benign Het
Exosc6 T A 8: 111,783,784 (GRCm39) V261E probably damaging Het
Fbxw17 C T 13: 50,586,300 (GRCm39) S361L probably benign Het
Gfap T A 11: 102,786,620 (GRCm39) N157Y possibly damaging Het
Gigyf2 A T 1: 87,307,725 (GRCm39) D177V unknown Het
Gls2 A T 10: 128,040,535 (GRCm39) Q312L probably benign Het
Gpr155 C T 2: 73,197,936 (GRCm39) V395I probably benign Het
Greb1l A T 18: 10,529,684 (GRCm39) M889L probably benign Het
Gucy1a1 T A 3: 82,016,049 (GRCm39) D313V probably damaging Het
H2-T5 T A 17: 36,476,293 (GRCm39) I324F probably benign Het
Herpud1 C T 8: 95,113,213 (GRCm39) probably benign Het
Idh2 TCCCAGG T 7: 79,748,079 (GRCm39) probably benign Het
Il27 A C 7: 126,190,194 (GRCm39) L140R probably damaging Het
Jarid2 T C 13: 45,055,984 (GRCm39) S397P possibly damaging Het
Kdm5a A C 6: 120,365,101 (GRCm39) D334A probably damaging Het
Lman2 T C 13: 55,496,197 (GRCm39) T283A probably benign Het
Lrfn2 C T 17: 49,378,277 (GRCm39) Q453* probably null Het
Lrrfip2 A G 9: 111,034,824 (GRCm39) E171G possibly damaging Het
Mboat1 T A 13: 30,410,397 (GRCm39) Y285N probably damaging Het
Med15 C A 16: 17,470,605 (GRCm39) S734I probably damaging Het
Mgat4c T A 10: 102,224,146 (GRCm39) I120N probably damaging Het
Ms4a4d T C 19: 11,530,251 (GRCm39) M104T possibly damaging Het
Mtf2 A T 5: 108,247,051 (GRCm39) M330L probably benign Het
Myoc T C 1: 162,475,013 (GRCm39) V188A probably benign Het
Nos2 T A 11: 78,839,949 (GRCm39) I686N probably damaging Het
Npffr1 T C 10: 61,461,794 (GRCm39) V310A probably benign Het
Nrap T C 19: 56,308,627 (GRCm39) *1729W probably null Het
Odam A G 5: 88,035,797 (GRCm39) probably null Het
Olfm4 G T 14: 80,258,943 (GRCm39) R397L probably damaging Het
Or1p1c T G 11: 74,160,120 (GRCm39) probably benign Het
Polr1b T C 2: 128,957,613 (GRCm39) V556A probably damaging Het
Prl3d3 A G 13: 27,346,324 (GRCm39) D186G possibly damaging Het
Psmc5 C A 11: 106,152,746 (GRCm39) Y189* probably null Het
Rasgrp4 A G 7: 28,838,521 (GRCm39) Y123C possibly damaging Het
Rtn4 A G 11: 29,658,633 (GRCm39) E929G probably benign Het
Scrn2 A T 11: 96,922,961 (GRCm39) I135F probably damaging Het
Sec24d T A 3: 123,148,585 (GRCm39) probably benign Het
Secisbp2l T C 2: 125,594,892 (GRCm39) T523A probably benign Het
Skic3 T C 13: 76,333,326 (GRCm39) L1525P probably damaging Het
Slain1 T A 14: 103,925,841 (GRCm39) probably null Het
Slc22a29 A G 19: 8,137,931 (GRCm39) V548A probably damaging Het
Slc25a32 T C 15: 38,969,339 (GRCm39) I65V probably benign Het
Slc30a7 A T 3: 115,740,317 (GRCm39) M378K possibly damaging Het
Smarcd1 T A 15: 99,608,975 (GRCm39) I383N probably damaging Het
Spata31h1 A T 10: 82,128,619 (GRCm39) S1464T probably benign Het
Spdye4b G T 5: 143,187,815 (GRCm39) K156N probably damaging Het
Sptb A G 12: 76,658,813 (GRCm39) Y1241H probably benign Het
Ssu2 G A 6: 112,357,956 (GRCm39) T129I probably damaging Het
Supt16 A G 14: 52,411,544 (GRCm39) V613A probably benign Het
Tatdn2 A T 6: 113,681,170 (GRCm39) Y401F probably damaging Het
Tigd4 T C 3: 84,501,547 (GRCm39) S155P probably benign Het
Tnrc6b A G 15: 80,802,290 (GRCm39) N1502S probably benign Het
Ttf2 A G 3: 100,870,644 (GRCm39) V143A probably benign Het
Ttn T A 2: 76,618,747 (GRCm39) D16179V probably damaging Het
Vmn2r106 A T 17: 20,488,401 (GRCm39) M666K probably benign Het
Vwa5b1 A T 4: 138,305,956 (GRCm39) V914D probably damaging Het
Wnk2 T C 13: 49,210,960 (GRCm39) M1632V probably benign Het
Zbtb26 T A 2: 37,326,913 (GRCm39) N41I probably damaging Het
Zc3h12a T C 4: 125,020,412 (GRCm39) N144D probably damaging Het
Zfp266 A T 9: 20,411,275 (GRCm39) C301S probably benign Het
Zfp580 A G 7: 5,056,216 (GRCm39) H192R possibly damaging Het
Zfp748 A G 13: 67,689,914 (GRCm39) C449R probably damaging Het
Zp2 T C 7: 119,733,025 (GRCm39) I612V probably benign Het
Other mutations in Sycp3
AlleleSourceChrCoordTypePredicted EffectPPH 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
R2858: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
R9163:Sycp3 UTSW 10 88,299,734 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- GCTGAACTCCTTGGTTCCTAAAT -3'
(R):5'- TCTCCACTGACTTCTAAGAAACATC -3'

Sequencing Primer
(F):5'- ATCTCCTTGATATTACTGAACAAACC -3'
(R):5'- ACATCAATTCTATGAAGGCATGAG -3'
Posted On 2021-07-15