Incidental Mutation 'R8141:Sycp1'
ID 632525
Institutional Source Beutler Lab
Gene Symbol Sycp1
Ensembl Gene ENSMUSG00000027855
Gene Name synaptonemal complex protein 1
Synonyms SCP1
MMRRC Submission 067569-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.539) question?
Stock # R8141 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 102725815-102843416 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 102842885 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Glutamic Acid at position 28 (A28E)
Ref Sequence ENSEMBL: ENSMUSP00000029448 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029448] [ENSMUST00000058899] [ENSMUST00000196988] [ENSMUST00000199930]
AlphaFold Q62209
Predicted Effect possibly damaging
Transcript: ENSMUST00000029448
AA Change: A28E

PolyPhen 2 Score 0.732 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: A28E

DomainStartEndE-ValueType
Pfam:SCP-1 28 809 N/A PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000058899
SMART Domains Protein: ENSMUSP00000052557
Gene: ENSMUSG00000048938

DomainStartEndE-ValueType
Blast:HOLI 2 47 5e-9 BLAST
ZnF_C4 119 190 2.51e-36 SMART
HOLI 289 474 1.74e-21 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000196988
AA Change: A28E

PolyPhen 2 Score 0.732 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: A28E

DomainStartEndE-ValueType
Pfam:SCP-1 28 809 N/A PFAM
Predicted Effect unknown
Transcript: ENSMUST00000199930
AA Change: A28E
SMART Domains Protein: ENSMUSP00000143493
Gene: ENSMUSG00000027855
AA Change: A28E

DomainStartEndE-ValueType
Pfam:SCP-1 28 95 2e-33 PFAM
Pfam:SCP-1 93 182 9.8e-53 PFAM
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.6%
  • 10x: 98.3%
  • 20x: 90.7%
Validation Efficiency 100% (59/59)
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: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700017B05Rik T C 9: 57,165,688 (GRCm39) T229A probably benign Het
4930438A08Rik A G 11: 58,177,411 (GRCm39) E40G Het
Actn2 T C 13: 12,303,516 (GRCm39) D428G probably damaging Het
Arl14epl C A 18: 47,059,410 (GRCm39) N8K probably benign Het
Bend7 T C 2: 4,757,636 (GRCm39) V226A probably benign Het
C1s1 A T 6: 124,508,321 (GRCm39) L556Q probably damaging Het
Casr T C 16: 36,315,173 (GRCm39) K966E probably damaging Het
Ccm2l T C 2: 152,912,791 (GRCm39) L110P probably damaging Het
Cdhr4 G A 9: 107,873,991 (GRCm39) R59H Het
Celf3 C A 3: 94,395,850 (GRCm39) N410K probably damaging Het
Cfap251 T G 5: 123,424,493 (GRCm39) V726G possibly damaging Het
Cpne6 T C 14: 55,750,066 (GRCm39) C66R possibly damaging Het
Cyp2f2 G A 7: 26,828,678 (GRCm39) V183I probably benign Het
Eln CTCCAGCTCCGAT C 5: 134,758,003 (GRCm39) probably benign Het
Fam53b A C 7: 132,361,758 (GRCm39) V90G probably damaging Het
Fat3 T A 9: 15,908,362 (GRCm39) I2547F possibly damaging Het
Foxk1 A G 5: 142,439,716 (GRCm39) Y524C probably damaging Het
Gpr87 A G 3: 59,087,020 (GRCm39) S162P probably damaging Het
Ifi204 A G 1: 173,583,189 (GRCm39) V343A possibly damaging Het
Igsf10 A G 3: 59,237,949 (GRCm39) L744P probably damaging Het
Iqub T A 6: 24,491,608 (GRCm39) K359N probably benign Het
Kdm3b A T 18: 34,961,599 (GRCm39) K1459* probably null Het
Kirrel1 C T 3: 86,993,735 (GRCm39) W507* probably null Het
Klra17 T C 6: 129,849,292 (GRCm39) D94G probably damaging Het
Llgl1 G C 11: 60,601,142 (GRCm39) E693D probably benign Het
Lrrc37 T C 11: 103,511,855 (GRCm39) T38A unknown Het
Lypd4 A T 7: 24,564,254 (GRCm39) D201E possibly damaging Het
Nin A G 12: 70,076,795 (GRCm39) S1794P Het
Oog2 T C 4: 143,920,777 (GRCm39) L70P probably damaging Het
Or6n2 T C 1: 173,897,488 (GRCm39) L208P probably damaging Het
Pacsin1 G T 17: 27,926,034 (GRCm39) R282S possibly damaging Het
Pcdhb9 T A 18: 37,535,361 (GRCm39) Y452N probably damaging Het
Pdgfra T C 5: 75,338,387 (GRCm39) V547A possibly damaging Het
Plcb4 T C 2: 135,781,169 (GRCm39) F209L probably damaging Het
Pnpla6 T C 8: 3,571,384 (GRCm39) S158P probably benign Het
Prlhr C G 19: 60,455,747 (GRCm39) R273P probably damaging Het
Prss41 G A 17: 24,056,607 (GRCm39) P196L probably damaging Het
Ptgr3 T C 18: 84,112,651 (GRCm39) L109P probably benign Het
Ptpn22 A G 3: 103,793,643 (GRCm39) E598G possibly damaging Het
Rasal2 T C 1: 156,992,240 (GRCm39) D569G possibly damaging Het
Sf3b3 A C 8: 111,547,483 (GRCm39) M715R possibly damaging Het
Ska1 T C 18: 74,339,907 (GRCm39) N13S probably benign Het
Spocd1 A C 4: 129,823,497 (GRCm39) E98A Het
Syf2 C T 4: 134,664,182 (GRCm39) R199C probably damaging Het
Syne2 A G 12: 76,108,442 (GRCm39) D942G possibly damaging Het
Tamalin T A 15: 101,129,790 (GRCm39) C358S possibly damaging Het
Tmem63a A G 1: 180,801,776 (GRCm39) T764A probably benign Het
Ttf1 C T 2: 28,957,238 (GRCm39) Q503* probably null Het
Usp13 T C 3: 32,949,025 (GRCm39) V454A possibly damaging Het
Usp47 A G 7: 111,652,472 (GRCm39) T50A possibly damaging Het
Zfyve26 A T 12: 79,315,331 (GRCm39) C1382S possibly damaging Het
Other mutations in Sycp1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- ACATACAAAGTGTAAGGCATGC -3'
(R):5'- ACGTACACACCTCTGTCACG -3'

Sequencing Primer
(F):5'- ACAAAGTGTAAGGCATGCTTTTC -3'
(R):5'- TGCAGGCTTTCACCGTG -3'
Posted On 2020-06-30