Incidental Mutation 'R7853:Sycp3'
ID 607080
Institutional Source Beutler Lab
Gene Symbol Sycp3
Ensembl Gene ENSMUSG00000020059
Gene Name synaptonemal complex protein 3
Synonyms Scp3, Cor1
MMRRC Submission 045906-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.127) question?
Stock # R7853 (G1)
Quality Score 225.009
Status Not validated
Chromosome 10
Chromosomal Location 88295449-88309098 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 88302368 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Asparagine at position 119 (K119N)
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: K119N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000020252
Gene: ENSMUSG00000020059
AA Change: K119N

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: K119N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000137800
Gene: ENSMUSG00000020059
AA Change: K119N

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: 99.9%
  • 10x: 99.6%
  • 20x: 98.8%
Validation Efficiency
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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921509C19Rik A G 2: 151,315,600 (GRCm39) I26T probably damaging Het
Aadacl4 G T 4: 144,344,592 (GRCm39) A123S probably benign Het
Adamts20 A C 15: 94,243,871 (GRCm39) C619G probably damaging Het
Ahcyl1 C A 3: 107,575,604 (GRCm39) V394L probably benign Het
Ankrd17 A C 5: 90,386,825 (GRCm39) L2378V possibly damaging Het
B3gnt3 T C 8: 72,145,357 (GRCm39) Y337C probably damaging Het
Bcl10 A G 3: 145,630,266 (GRCm39) K18R possibly damaging Het
Calcr G A 6: 3,707,499 (GRCm39) A267V probably benign Het
Ces1d C T 8: 93,901,695 (GRCm39) G425S probably benign Het
Col1a1 G T 11: 94,838,505 (GRCm39) R899L unknown Het
Commd1 C T 11: 22,906,532 (GRCm39) R168H possibly damaging Het
Cps1 T C 1: 67,213,640 (GRCm39) S791P possibly damaging Het
Ctsj T A 13: 61,151,884 (GRCm39) I58F probably damaging Het
Cyp2j5 T A 4: 96,529,656 (GRCm39) K238N probably benign Het
Dlgap4 A G 2: 156,547,802 (GRCm39) D423G probably benign Het
Eef1ece2 T A 16: 20,463,010 (GRCm39) probably null Het
Egln1 T C 8: 125,675,256 (GRCm39) N180D probably benign Het
Ehd1 T C 19: 6,327,225 (GRCm39) F74S probably damaging Het
Ext1 G A 15: 52,970,881 (GRCm39) A350V probably damaging Het
Fam186b T A 15: 99,178,628 (GRCm39) I233F probably damaging Het
Fam193a T G 5: 34,597,473 (GRCm39) N91K probably benign Het
Far1 T A 7: 113,153,355 (GRCm39) N329K probably damaging Het
Fhad1 A G 4: 141,637,134 (GRCm39) S1111P probably damaging Het
Fhl2 A G 1: 43,180,984 (GRCm39) S69P probably damaging Het
Flg2 C A 3: 93,128,054 (GRCm39) P2322Q unknown Het
Flvcr1 A G 1: 190,757,843 (GRCm39) Y108H probably damaging Het
Fos T A 12: 85,522,792 (GRCm39) S235T probably benign Het
Foxf1 T A 8: 121,811,438 (GRCm39) S101T probably damaging Het
Gfer C A 17: 24,913,259 (GRCm39) D198Y probably damaging Het
Ggps1 T C 13: 14,229,034 (GRCm39) I50V probably benign Het
Gkn2 A G 6: 87,355,255 (GRCm39) T155A probably benign Het
Gna12 C T 5: 140,746,449 (GRCm39) C332Y probably damaging Het
Hc T A 2: 34,900,045 (GRCm39) Y1096F probably damaging Het
Hoxa3 G A 6: 52,147,267 (GRCm39) probably benign Het
Hsd17b8 T G 17: 34,246,411 (GRCm39) D117A probably benign Het
Ifi206 A T 1: 173,299,100 (GRCm39) Y835* probably null Het
Ighv13-2 T G 12: 114,321,544 (GRCm39) E65A probably damaging Het
Kif5a A T 10: 127,071,537 (GRCm39) Y770* probably null Het
Lfng A G 5: 140,593,384 (GRCm39) S72G probably benign Het
Lipo2 C T 19: 33,737,344 (GRCm39) probably benign Het
Lnpep C T 17: 17,783,109 (GRCm39) S564N probably benign Het
Mfhas1 T A 8: 36,057,025 (GRCm39) L500* probably null Het
Mllt6 G A 11: 97,561,142 (GRCm39) V277I probably benign Het
Mroh5 C T 15: 73,663,189 (GRCm39) D192N probably benign Het
Myo1f T A 17: 33,795,672 (GRCm39) V106D probably damaging Het
Mypn T A 10: 62,981,652 (GRCm39) I643F probably benign Het
Nup188 A G 2: 30,213,575 (GRCm39) N669D possibly damaging Het
Or14j5 C G 17: 38,161,714 (GRCm39) T77R probably damaging Het
Or2r11 A T 6: 42,437,573 (GRCm39) C127S probably damaging Het
Or5g26 T C 2: 85,494,689 (GRCm39) T30A probably benign Het
Or8s8 T C 15: 98,354,866 (GRCm39) V225A probably benign Het
Osbpl10 A G 9: 115,036,726 (GRCm39) T241A probably damaging Het
Peg3 C T 7: 6,711,839 (GRCm39) E1128K possibly damaging Het
Plch1 C A 3: 63,681,068 (GRCm39) M186I probably benign Het
Pon3 A C 6: 5,236,911 (GRCm39) L152R probably damaging Het
Prr36 G A 8: 4,263,905 (GRCm39) P587L unknown Het
Psma2 T A 13: 14,799,832 (GRCm39) I192N probably damaging Het
Rbm11 T C 16: 75,389,923 (GRCm39) F30L probably damaging Het
Rpap3 G A 15: 97,576,299 (GRCm39) A622V possibly damaging Het
Scgb2b11 T A 7: 31,908,807 (GRCm39) N98Y probably damaging Het
Siglec1 A G 2: 130,923,212 (GRCm39) L511P probably damaging Het
Sirpb1c C T 3: 15,887,156 (GRCm39) V228M probably damaging Het
Smpd4 T A 16: 17,460,605 (GRCm39) Y804N probably damaging Het
Sult6b2 T C 6: 142,747,524 (GRCm39) D75G not run Het
Syne2 T C 12: 76,078,278 (GRCm39) L4703P probably damaging Het
Tex12 C G 9: 50,470,523 (GRCm39) L20F possibly damaging Het
Them5 T A 3: 94,250,603 (GRCm39) Y55* probably null Het
Tmem43 A T 6: 91,458,968 (GRCm39) D213V probably benign Het
Tnfrsf10b A C 14: 70,005,239 (GRCm39) Q44P unknown Het
Trbv2 A T 6: 41,024,836 (GRCm39) Q84L probably benign Het
Trim2 C T 3: 84,212,537 (GRCm39) probably benign Het
Trim36 A G 18: 46,305,558 (GRCm39) V475A probably benign Het
Ttbk1 C A 17: 46,758,269 (GRCm39) E788D probably benign Het
Ttn T C 2: 76,543,626 (GRCm39) D33120G probably damaging Het
Ttn T A 2: 76,576,256 (GRCm39) N24879I probably damaging Het
Ube4a T A 9: 44,864,308 (GRCm39) Q76L probably benign Het
Vmn2r27 T A 6: 124,168,980 (GRCm39) I717F probably damaging Het
Vmn2r45 T C 7: 8,485,987 (GRCm39) K434E possibly damaging Het
Vta1 T C 10: 14,531,461 (GRCm39) T305A probably damaging Het
Zfp354c TCACACTCGGCACA TCACA 11: 50,706,067 (GRCm39) 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
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'- TGCTGAACTCCTTGGTTCCTAA -3'
(R):5'- CACATTTTGGCATGGTAAGGAT -3'

Sequencing Primer
(F):5'- CCTTGATATTACTGAACAAACCT -3'
(R):5'- ACATCAATTCTATGAAGGCATGAG -3'
Posted On 2019-12-20