Incidental Mutation 'R4007:Syce1'
ID 311526
Institutional Source Beutler Lab
Gene Symbol Syce1
Ensembl Gene ENSMUSG00000025480
Gene Name synaptonemal complex central element protein 1
Synonyms 4933406J07Rik
MMRRC Submission 041610-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4007 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 140357142-140367765 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 140359809 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Phenylalanine at position 83 (L83F)
Ref Sequence ENSEMBL: ENSMUSP00000148137 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026552] [ENSMUST00000026553] [ENSMUST00000209253] [ENSMUST00000211616]
AlphaFold Q9D495
Predicted Effect probably benign
Transcript: ENSMUST00000026552
SMART Domains Protein: ENSMUSP00000026552
Gene: ENSMUSG00000025479

DomainStartEndE-ValueType
transmembrane domain 2 23 N/A INTRINSIC
Pfam:p450 33 489 1.4e-147 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000026553
AA Change: L104F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000026553
Gene: ENSMUSG00000025480
AA Change: L104F

DomainStartEndE-ValueType
Pfam:SYCE1 49 200 5.5e-66 PFAM
coiled coil region 237 294 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204061
Predicted Effect probably benign
Transcript: ENSMUST00000209253
Predicted Effect probably damaging
Transcript: ENSMUST00000211616
AA Change: L83F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Meta Mutation Damage Score 0.1033 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 93.8%
Validation Efficiency 98% (49/50)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the synaptonemal complex, which links homologous chromosomes during prophase I of meiosis. The tripartite structure of the complex is highly conserved amongst metazoans. It consists of two lateral elements and a central region formed by transverse elements and a central element. The protein encoded by this gene localizes to the central element and is required for initiation and elongation of the synapsis. Allelic variants of this gene have been associated with premature ovarian failure and spermatogenic failure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
PHENOTYPE: Mice homozygous for a null allele exhibit small ovaries and small testes, severe defects in gametogenesis, and infertility in both sexes. Meiosis is arrested, homologous chromosomes fail to synapse, and meiotic double-strand breaks are formed but are notefficiently repaired. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A1cf T C 19: 31,895,524 (GRCm39) probably null Het
Aff1 A T 5: 103,932,088 (GRCm39) K243N probably benign Het
Aknad1 T C 3: 108,682,598 (GRCm39) I558T probably benign Het
Ampd1 A G 3: 102,999,776 (GRCm39) I460V probably damaging Het
Atp10b A T 11: 43,150,679 (GRCm39) H1459L probably benign Het
Card9 T A 2: 26,243,012 (GRCm39) R459W possibly damaging Het
Chd3 A T 11: 69,239,827 (GRCm39) I1667N probably benign Het
Col6a3 A G 1: 90,730,291 (GRCm39) S1672P probably damaging Het
Cul4a A G 8: 13,172,859 (GRCm39) N164S probably benign Het
Dhx37 G A 5: 125,501,995 (GRCm39) probably benign Het
Dnah1 T C 14: 31,025,741 (GRCm39) probably benign Het
Elp1 G A 4: 56,794,139 (GRCm39) T168I probably damaging Het
Erbb4 C A 1: 68,779,560 (GRCm39) R72L probably damaging Het
F11r A G 1: 171,288,916 (GRCm39) K178R probably benign Het
Fan1 A G 7: 64,016,309 (GRCm39) L605P probably damaging Het
Fcna A G 2: 25,516,018 (GRCm39) probably null Het
Filip1 A G 9: 79,726,009 (GRCm39) I870T possibly damaging Het
Gm11595 C T 11: 99,662,861 (GRCm39) C273Y unknown Het
Gml T A 15: 74,685,548 (GRCm39) I146L possibly damaging Het
Gprc5b G A 7: 118,583,437 (GRCm39) A144V possibly damaging Het
Htr2a A T 14: 74,879,581 (GRCm39) H70L probably benign Het
Ifitm6 T A 7: 140,596,627 (GRCm39) I69F possibly damaging Het
Iqsec3 A G 6: 121,353,187 (GRCm39) S1144P probably damaging Het
Kazn T C 4: 141,834,203 (GRCm39) T618A unknown Het
Mrps5 C A 2: 127,433,755 (GRCm39) T48K possibly damaging Het
Mst1 A G 9: 107,960,147 (GRCm39) E377G possibly damaging Het
Nup188 G A 2: 30,199,890 (GRCm39) D305N probably damaging Het
Opn4 A T 14: 34,321,789 (GRCm39) S43T probably benign Het
Or8k35 T C 2: 86,424,908 (GRCm39) D88G probably benign Het
Plcb2 T C 2: 118,541,274 (GRCm39) E1021G probably damaging Het
Pramex1 A T X: 134,514,374 (GRCm39) L305Q probably damaging Het
Rbsn T A 6: 92,166,800 (GRCm39) T615S probably benign Het
Reg1 A G 6: 78,404,013 (GRCm39) D60G probably null Het
Ros1 A T 10: 51,994,328 (GRCm39) D1317E probably damaging Het
Rpap2 A G 5: 107,751,738 (GRCm39) I129V probably damaging Het
Rubcnl G T 14: 75,287,143 (GRCm39) V604L possibly damaging Het
Slc26a4 T A 12: 31,590,532 (GRCm39) K374* probably null Het
Slc4a4 T A 5: 89,362,452 (GRCm39) S854R probably damaging Het
Sv2c A G 13: 96,123,341 (GRCm39) probably benign Het
Tnik A G 3: 28,658,430 (GRCm39) S572G probably damaging Het
Trbv13-3 T C 6: 41,107,120 (GRCm39) C14R probably benign Het
Ttc7 G A 17: 87,597,679 (GRCm39) D84N possibly damaging Het
Ubtd1 G T 19: 42,020,555 (GRCm39) G100* probably null Het
Vmn2r18 A T 5: 151,508,711 (GRCm39) W138R probably damaging Het
Zan T C 5: 137,462,201 (GRCm39) T993A unknown Het
Zfp385b C T 2: 77,549,836 (GRCm39) G83D probably benign Het
Zfp493 A G 13: 67,932,038 (GRCm39) probably benign Het
Other mutations in Syce1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02112:Syce1 APN 7 140,359,545 (GRCm39) missense probably benign
IGL03304:Syce1 APN 7 140,357,623 (GRCm39) missense possibly damaging 0.67
R0918:Syce1 UTSW 7 140,360,436 (GRCm39) missense probably damaging 1.00
R1106:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R1169:Syce1 UTSW 7 140,358,120 (GRCm39) missense probably benign 0.00
R1430:Syce1 UTSW 7 140,359,351 (GRCm39) unclassified probably benign
R1436:Syce1 UTSW 7 140,357,593 (GRCm39) missense possibly damaging 0.84
R1650:Syce1 UTSW 7 140,358,300 (GRCm39) missense possibly damaging 0.62
R2081:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R2082:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R3890:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R3891:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4006:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4077:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4078:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4079:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R4817:Syce1 UTSW 7 140,358,336 (GRCm39) missense probably benign 0.00
R4824:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
R5040:Syce1 UTSW 7 140,358,978 (GRCm39) missense probably damaging 1.00
R5766:Syce1 UTSW 7 140,357,894 (GRCm39) missense probably damaging 1.00
R6380:Syce1 UTSW 7 140,358,978 (GRCm39) missense probably damaging 1.00
R7048:Syce1 UTSW 7 140,359,281 (GRCm39) missense possibly damaging 0.73
R8681:Syce1 UTSW 7 140,361,987 (GRCm39) missense possibly damaging 0.58
Y4338:Syce1 UTSW 7 140,359,809 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCCTCTGAGTGCTTGCTAAG -3'
(R):5'- TTTACAGGAATGTGGATACCCG -3'

Sequencing Primer
(F):5'- ACATATCACATCAAGTCTGTGGAC -3'
(R):5'- CGTAGGGGTAGGAACTTACCTC -3'
Posted On 2015-04-29