Incidental Mutation 'R2483:Sycp2'
ID 250632
Institutional Source Beutler Lab
Gene Symbol Sycp2
Ensembl Gene ENSMUSG00000060445
Gene Name synaptonemal complex protein 2
Synonyms 3830402K23Rik, 4930518F03Rik
MMRRC Submission 040407-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2483 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 177987086-178049478 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 178016388 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 691 (N691K)
Ref Sequence ENSEMBL: ENSMUSP00000079909 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000081134]
AlphaFold Q9CUU3
Predicted Effect probably damaging
Transcript: ENSMUST00000081134
AA Change: N691K

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000079909
Gene: ENSMUSG00000060445
AA Change: N691K

DomainStartEndE-ValueType
low complexity region 945 960 N/A INTRINSIC
low complexity region 1006 1019 N/A INTRINSIC
low complexity region 1076 1091 N/A INTRINSIC
low complexity region 1195 1204 N/A INTRINSIC
low complexity region 1273 1293 N/A INTRINSIC
low complexity region 1355 1364 N/A INTRINSIC
coiled coil region 1387 1429 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132611
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132765
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.5%
  • 20x: 95.6%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The synaptonemal complex is a proteinaceous structure that links homologous chromosomes during the prophase of meiosis. The protein encoded by this gene is a major component of the synaptonemal complex and may bind DNA at scaffold attachment regions. The encoded protein requires synaptonemal complex protein 3, but not 1, for inclusion in the synaptonemal complex. [provided by RefSeq, Jul 2008]
PHENOTYPE: Male mice homozygous for a knock-out allele are sterile due to lack of axial element formation and subsequent failure of chromosome synapsis in prophase I spermatocytes, while females are subfertile with a sharply reduced litter size. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adcy1 A G 11: 7,080,348 (GRCm39) T364A probably benign Het
Adpgk G A 9: 59,221,036 (GRCm39) V281I probably benign Het
Akap9 C A 5: 4,026,235 (GRCm39) Q1297K possibly damaging Het
Ankrd13d T C 19: 4,331,968 (GRCm39) E110G probably damaging Het
Ankrd53 A G 6: 83,740,244 (GRCm39) E104G possibly damaging Het
Ano6 A T 15: 95,863,855 (GRCm39) T792S probably benign Het
Atm A T 9: 53,421,566 (GRCm39) V715D probably damaging Het
Avl9 A G 6: 56,713,828 (GRCm39) D362G probably benign Het
Bin1 T A 18: 32,547,280 (GRCm39) S152R probably damaging Het
Bscl2 T A 19: 8,818,514 (GRCm39) C40S probably benign Het
Btaf1 A G 19: 36,958,486 (GRCm39) T668A probably benign Het
Btrc A G 19: 45,504,497 (GRCm39) D397G probably damaging Het
Cables2 A T 2: 179,902,222 (GRCm39) V379E probably damaging Het
Cacna2d2 T C 9: 107,389,221 (GRCm39) L228P probably damaging Het
Cd109 A T 9: 78,574,639 (GRCm39) D541V probably damaging Het
Cdh26 A T 2: 178,108,382 (GRCm39) S327C probably damaging Het
Cep78 T C 19: 15,938,344 (GRCm39) K535E probably damaging Het
Ces1a A G 8: 93,753,969 (GRCm39) Y345H probably damaging Het
Col6a5 C A 9: 105,741,347 (GRCm39) R2524I probably damaging Het
Cracd A T 5: 77,004,256 (GRCm39) I206F probably damaging Het
Dctn1 G A 6: 83,171,169 (GRCm39) R661H probably damaging Het
Ddias T C 7: 92,508,800 (GRCm39) T372A probably benign Het
Dffb T C 4: 154,049,976 (GRCm39) T296A probably damaging Het
Dock8 A G 19: 25,057,241 (GRCm39) Q216R probably benign Het
Emx1 T C 6: 85,165,237 (GRCm39) S105P probably benign Het
Ep400 T C 5: 110,867,102 (GRCm39) Y1014C unknown Het
Fam193a A T 5: 34,623,102 (GRCm39) K1230M possibly damaging Het
Fgf9 A G 14: 58,347,028 (GRCm39) Q207R probably benign Het
Gm5460 G A 14: 33,767,775 (GRCm39) C461Y possibly damaging Het
Gpc1 T C 1: 92,783,660 (GRCm39) I249T probably benign Het
Htr1d T C 4: 136,170,815 (GRCm39) I348T probably damaging Het
Hyal4 A T 6: 24,765,737 (GRCm39) S364C probably damaging Het
Igfn1 T C 1: 135,897,275 (GRCm39) E1097G probably benign Het
Igkv1-133 A T 6: 67,701,944 (GRCm39) Q16L probably benign Het
Kcnh5 A T 12: 75,161,245 (GRCm39) I221N probably damaging Het
Kmt2a A G 9: 44,760,263 (GRCm39) Y529H probably damaging Het
Kyat1 T C 2: 30,076,710 (GRCm39) H218R possibly damaging Het
Lamb2 T G 9: 108,357,758 (GRCm39) C94G probably damaging Het
Met A T 6: 17,549,085 (GRCm39) D979V probably damaging Het
Midn A G 10: 79,986,144 (GRCm39) D78G probably benign Het
Myh1 A T 11: 67,102,052 (GRCm39) M811L probably benign Het
Myh7 T C 14: 55,210,838 (GRCm39) E1693G probably damaging Het
Myo15b A G 11: 115,755,565 (GRCm39) T979A probably benign Het
Myo18b A T 5: 113,006,274 (GRCm39) C879S probably damaging Het
Myom1 A G 17: 71,384,807 (GRCm39) T733A probably damaging Het
Ndufa9 A T 6: 126,821,362 (GRCm39) M76K possibly damaging Het
Nectin3 A G 16: 46,215,542 (GRCm39) C74R possibly damaging Het
Obscn A G 11: 58,970,972 (GRCm39) F2514L probably damaging Het
Or4a69 G A 2: 89,313,471 (GRCm39) Q3* probably null Het
Or52d3 T C 7: 104,229,149 (GRCm39) S99P probably damaging Het
Or5p81 CAAATA CA 7: 108,266,869 (GRCm39) probably null Het
P2ry2 A T 7: 100,647,706 (GRCm39) S200T probably benign Het
Pcdha5 G T 18: 37,094,542 (GRCm39) M350I probably benign Het
Pcdha5 G A 18: 37,094,834 (GRCm39) V448M probably damaging Het
Pex12 C T 11: 83,188,455 (GRCm39) R180H possibly damaging Het
Pip4p1 C G 14: 51,167,749 (GRCm39) V59L probably damaging Het
Pkd1l1 A T 11: 8,912,701 (GRCm39) V168E probably damaging Het
Prokr2 T A 2: 132,223,095 (GRCm39) D149V probably damaging Het
Rnf123 A G 9: 107,940,720 (GRCm39) V707A probably benign Het
Ryr2 T C 13: 11,774,589 (GRCm39) E1189G probably damaging Het
Scarf1 T C 11: 75,406,117 (GRCm39) F134L probably damaging Het
Sfxn5 A G 6: 85,309,260 (GRCm39) probably null Het
Shfl A T 9: 20,784,473 (GRCm39) I186F possibly damaging Het
Skic3 A G 13: 76,330,986 (GRCm39) E1472G probably damaging Het
Slc17a5 A T 9: 78,445,556 (GRCm39) V433D probably damaging Het
Snapc1 A G 12: 74,011,417 (GRCm39) T28A probably benign Het
Soat1 T C 1: 156,258,669 (GRCm39) Y528C probably damaging Het
Spem1 G A 11: 69,712,344 (GRCm39) R107C possibly damaging Het
Srcap T C 7: 127,141,319 (GRCm39) S1639P probably damaging Het
Syne2 A T 12: 76,142,311 (GRCm39) I6183F probably damaging Het
Tas2r110 A T 6: 132,845,433 (GRCm39) M155L probably benign Het
Tenm3 G A 8: 48,693,305 (GRCm39) T1859I probably damaging Het
Thsd7b T A 1: 130,030,809 (GRCm39) V1048D probably damaging Het
Vav3 T C 3: 109,248,482 (GRCm39) L43P probably damaging Het
Vmn1r30 A T 6: 58,412,437 (GRCm39) F132I probably benign Het
Vmn2r24 A G 6: 123,792,997 (GRCm39) R775G probably damaging Het
Vps13c T A 9: 67,883,189 (GRCm39) probably null Het
Vps37c T A 19: 10,683,569 (GRCm39) probably null Het
Wwp2 A G 8: 108,275,167 (GRCm39) D388G probably damaging Het
Xirp2 A T 2: 67,355,336 (GRCm39) T3366S probably benign Het
Zbtb49 A C 5: 38,360,701 (GRCm39) probably benign Het
Other mutations in Sycp2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00484:Sycp2 APN 2 178,024,141 (GRCm39) missense probably damaging 1.00
IGL00578:Sycp2 APN 2 177,992,615 (GRCm39) splice site probably benign
IGL00646:Sycp2 APN 2 178,016,252 (GRCm39) missense probably benign 0.00
IGL01309:Sycp2 APN 2 177,999,904 (GRCm39) missense probably benign 0.15
IGL01464:Sycp2 APN 2 178,043,425 (GRCm39) missense probably damaging 0.96
IGL01539:Sycp2 APN 2 178,016,488 (GRCm39) missense probably damaging 1.00
IGL01670:Sycp2 APN 2 178,019,843 (GRCm39) missense probably benign 0.00
IGL02138:Sycp2 APN 2 178,043,783 (GRCm39) nonsense probably null
IGL02138:Sycp2 APN 2 178,000,047 (GRCm39) missense probably benign 0.31
IGL02630:Sycp2 APN 2 178,043,712 (GRCm39) missense probably damaging 1.00
IGL02673:Sycp2 APN 2 178,036,004 (GRCm39) missense possibly damaging 0.63
IGL02961:Sycp2 APN 2 178,022,655 (GRCm39) missense probably benign 0.01
IGL03084:Sycp2 APN 2 178,033,584 (GRCm39) unclassified probably benign
IGL03123:Sycp2 APN 2 177,994,272 (GRCm39) nonsense probably null
IGL03167:Sycp2 APN 2 178,021,291 (GRCm39) missense probably damaging 0.99
R0043:Sycp2 UTSW 2 178,006,504 (GRCm39) missense probably damaging 1.00
R0050:Sycp2 UTSW 2 178,006,504 (GRCm39) missense probably damaging 1.00
R0096:Sycp2 UTSW 2 178,045,528 (GRCm39) missense probably damaging 0.99
R0096:Sycp2 UTSW 2 178,045,528 (GRCm39) missense probably damaging 0.99
R0310:Sycp2 UTSW 2 178,023,648 (GRCm39) missense probably benign 0.44
R0363:Sycp2 UTSW 2 177,988,204 (GRCm39) splice site probably benign
R0456:Sycp2 UTSW 2 178,023,648 (GRCm39) missense probably benign 0.44
R0597:Sycp2 UTSW 2 177,998,373 (GRCm39) missense possibly damaging 0.54
R0608:Sycp2 UTSW 2 178,024,197 (GRCm39) missense probably damaging 0.98
R1112:Sycp2 UTSW 2 177,994,329 (GRCm39) missense probably benign 0.05
R1127:Sycp2 UTSW 2 178,016,159 (GRCm39) missense possibly damaging 0.72
R1208:Sycp2 UTSW 2 177,998,421 (GRCm39) missense possibly damaging 0.92
R1208:Sycp2 UTSW 2 177,998,421 (GRCm39) missense possibly damaging 0.92
R1323:Sycp2 UTSW 2 177,989,414 (GRCm39) missense possibly damaging 0.50
R1323:Sycp2 UTSW 2 177,989,414 (GRCm39) missense possibly damaging 0.50
R1413:Sycp2 UTSW 2 177,989,590 (GRCm39) missense probably benign 0.00
R1557:Sycp2 UTSW 2 178,037,009 (GRCm39) unclassified probably benign
R1562:Sycp2 UTSW 2 178,024,178 (GRCm39) missense probably damaging 1.00
R1585:Sycp2 UTSW 2 177,993,461 (GRCm39) missense possibly damaging 0.50
R1932:Sycp2 UTSW 2 178,023,750 (GRCm39) missense probably damaging 1.00
R1950:Sycp2 UTSW 2 178,044,593 (GRCm39) missense probably benign 0.00
R2001:Sycp2 UTSW 2 178,019,848 (GRCm39) missense probably benign 0.05
R2105:Sycp2 UTSW 2 177,991,931 (GRCm39) splice site probably null
R2382:Sycp2 UTSW 2 178,019,811 (GRCm39) critical splice donor site probably null
R2403:Sycp2 UTSW 2 178,045,528 (GRCm39) nonsense probably null
R3003:Sycp2 UTSW 2 177,999,916 (GRCm39) missense probably benign 0.01
R3418:Sycp2 UTSW 2 178,043,446 (GRCm39) splice site probably benign
R3686:Sycp2 UTSW 2 178,016,177 (GRCm39) missense probably benign 0.16
R4038:Sycp2 UTSW 2 178,022,720 (GRCm39) missense possibly damaging 0.72
R4039:Sycp2 UTSW 2 178,022,720 (GRCm39) missense possibly damaging 0.72
R4272:Sycp2 UTSW 2 178,000,017 (GRCm39) missense probably benign 0.04
R4343:Sycp2 UTSW 2 178,022,740 (GRCm39) missense probably damaging 0.99
R4491:Sycp2 UTSW 2 178,016,778 (GRCm39) missense probably damaging 1.00
R4534:Sycp2 UTSW 2 177,996,802 (GRCm39) missense probably damaging 1.00
R4720:Sycp2 UTSW 2 178,016,225 (GRCm39) missense probably benign 0.11
R4805:Sycp2 UTSW 2 178,035,754 (GRCm39) unclassified probably benign
R4807:Sycp2 UTSW 2 178,035,754 (GRCm39) unclassified probably benign
R4808:Sycp2 UTSW 2 178,035,754 (GRCm39) unclassified probably benign
R4906:Sycp2 UTSW 2 178,045,450 (GRCm39) critical splice donor site probably null
R4910:Sycp2 UTSW 2 178,000,017 (GRCm39) missense probably benign 0.04
R5282:Sycp2 UTSW 2 178,045,554 (GRCm39) missense probably damaging 1.00
R5285:Sycp2 UTSW 2 178,034,191 (GRCm39) splice site probably null
R5316:Sycp2 UTSW 2 177,998,296 (GRCm39) missense probably benign 0.00
R5389:Sycp2 UTSW 2 178,019,495 (GRCm39) splice site probably null
R5621:Sycp2 UTSW 2 178,023,711 (GRCm39) missense probably benign 0.05
R5652:Sycp2 UTSW 2 178,000,498 (GRCm39) splice site probably null
R5880:Sycp2 UTSW 2 178,016,263 (GRCm39) missense possibly damaging 0.92
R6114:Sycp2 UTSW 2 177,990,038 (GRCm39) missense probably benign 0.25
R6115:Sycp2 UTSW 2 177,990,038 (GRCm39) missense probably benign 0.25
R6186:Sycp2 UTSW 2 178,025,353 (GRCm39) missense probably damaging 0.97
R6351:Sycp2 UTSW 2 178,005,209 (GRCm39) missense probably damaging 1.00
R6509:Sycp2 UTSW 2 178,037,687 (GRCm39) missense probably damaging 1.00
R6536:Sycp2 UTSW 2 177,993,441 (GRCm39) missense probably damaging 1.00
R6679:Sycp2 UTSW 2 178,022,721 (GRCm39) missense probably damaging 0.96
R6687:Sycp2 UTSW 2 177,996,753 (GRCm39) missense probably damaging 0.99
R6761:Sycp2 UTSW 2 178,016,144 (GRCm39) splice site probably null
R6786:Sycp2 UTSW 2 178,025,345 (GRCm39) missense possibly damaging 0.63
R7357:Sycp2 UTSW 2 178,045,597 (GRCm39) splice site probably null
R7422:Sycp2 UTSW 2 178,035,944 (GRCm39) missense probably damaging 1.00
R7519:Sycp2 UTSW 2 177,988,126 (GRCm39) makesense probably null
R7805:Sycp2 UTSW 2 178,022,651 (GRCm39) missense probably damaging 0.99
R7960:Sycp2 UTSW 2 178,046,453 (GRCm39) missense probably null 0.90
R8022:Sycp2 UTSW 2 177,996,855 (GRCm39) missense probably damaging 1.00
R8037:Sycp2 UTSW 2 178,045,571 (GRCm39) missense probably damaging 1.00
R8038:Sycp2 UTSW 2 178,045,571 (GRCm39) missense probably damaging 1.00
R8039:Sycp2 UTSW 2 178,016,378 (GRCm39) missense probably benign 0.05
R8159:Sycp2 UTSW 2 177,996,770 (GRCm39) missense probably damaging 0.97
R8233:Sycp2 UTSW 2 177,998,427 (GRCm39) missense probably damaging 1.00
R8436:Sycp2 UTSW 2 178,004,761 (GRCm39) missense probably benign 0.44
R8437:Sycp2 UTSW 2 178,006,651 (GRCm39) missense probably damaging 1.00
R8528:Sycp2 UTSW 2 178,016,326 (GRCm39) missense probably damaging 1.00
R8679:Sycp2 UTSW 2 177,992,768 (GRCm39) missense probably damaging 0.99
R8711:Sycp2 UTSW 2 177,990,088 (GRCm39) missense probably benign 0.41
R8843:Sycp2 UTSW 2 177,990,052 (GRCm39) missense probably damaging 0.99
R9044:Sycp2 UTSW 2 177,989,617 (GRCm39) missense probably damaging 1.00
R9067:Sycp2 UTSW 2 177,989,214 (GRCm39) critical splice donor site probably null
R9203:Sycp2 UTSW 2 177,996,906 (GRCm39) missense probably damaging 1.00
R9263:Sycp2 UTSW 2 178,035,931 (GRCm39) missense probably damaging 1.00
R9301:Sycp2 UTSW 2 178,023,650 (GRCm39) missense probably benign 0.00
R9596:Sycp2 UTSW 2 177,990,212 (GRCm39) critical splice donor site probably null
R9633:Sycp2 UTSW 2 177,998,254 (GRCm39) missense probably damaging 1.00
R9715:Sycp2 UTSW 2 178,035,957 (GRCm39) missense probably damaging 1.00
R9748:Sycp2 UTSW 2 178,025,304 (GRCm39) missense probably damaging 1.00
Z1088:Sycp2 UTSW 2 178,023,727 (GRCm39) missense probably benign 0.17
Z1088:Sycp2 UTSW 2 178,016,160 (GRCm39) missense probably benign
Z1176:Sycp2 UTSW 2 178,006,674 (GRCm39) missense probably damaging 1.00
Z1177:Sycp2 UTSW 2 178,022,668 (GRCm39) missense probably damaging 1.00
Z1191:Sycp2 UTSW 2 177,992,662 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- AGTTCAGACATCAGTTCCTTTCTTG -3'
(R):5'- ATTCTTCCACTAGATACTGGTGTCAAC -3'

Sequencing Primer
(F):5'- AGACATCAGTTCCTTTCTTGATTTTG -3'
(R):5'- CAGTATCAGATGATGATTCTGA -3'
Posted On 2014-12-04