Incidental Mutation 'R1106:Syce1'
ID 98476
Institutional Source Beutler Lab
Gene Symbol Syce1
Ensembl Gene ENSMUSG00000025480
Gene Name synaptonemal complex central element protein 1
Synonyms 4933406J07Rik
MMRRC Submission 039179-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1106 (G1)
Quality Score 225
Status Not 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: 98.3%
  • 10x: 96.3%
  • 20x: 92.5%
Validation Efficiency
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: 20 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Asic5 C A 3: 81,911,897 (GRCm39) F122L probably damaging Het
Caml A G 13: 55,772,538 (GRCm39) T61A probably benign Het
Cfap20 A T 8: 96,147,873 (GRCm39) I156N probably damaging Het
Col1a2 G A 6: 4,518,822 (GRCm39) probably benign Het
Dio2 A G 12: 90,704,985 (GRCm39) L25P probably damaging Het
Eps8 G A 6: 137,491,322 (GRCm39) P352L probably damaging Het
Gnai2 A G 9: 107,497,385 (GRCm39) I3T probably damaging Het
Hexim2 T C 11: 103,029,319 (GRCm39) S124P probably damaging Het
Klk1b16 C T 7: 43,788,937 (GRCm39) R57C probably damaging Het
Mier3 A T 13: 111,844,763 (GRCm39) D205V probably damaging Het
Or2y14 A G 11: 49,404,519 (GRCm39) D18G probably damaging Het
Or4c102 T C 2: 88,422,355 (GRCm39) V69A probably benign Het
Ptprz1 A G 6: 22,965,748 (GRCm39) D192G probably damaging Het
Samd3 G A 10: 26,147,689 (GRCm39) V455M possibly damaging Het
Slc9c1 C A 16: 45,376,170 (GRCm39) Q419K possibly damaging Het
Tas2r139 A G 6: 42,118,479 (GRCm39) T204A probably benign Het
Ush2a G A 1: 188,643,180 (GRCm39) E4181K possibly damaging Het
Vps37a T A 8: 40,965,247 (GRCm39) I33N probably damaging Het
Zfp335 TTGCTGCTGCTGCTGCTGCT TTGCTGCTGCTGCTGCT 2: 164,749,471 (GRCm39) probably benign Het
Zik1 G A 7: 10,224,312 (GRCm39) R262C probably damaging 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
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
R4007: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'- TGCAGGCATGGCATCTTACCTC -3'
(R):5'- AGTTATTGCCTCACACCAGCAGC -3'

Sequencing Primer
(F):5'- CCTCAGGGTCTCTGTAAGGATAAC -3'
(R):5'- TTTACAGGAATGTGGATACCCG -3'
Posted On 2014-01-05