Incidental Mutation 'R6242:Spc25'
ID 505274
Institutional Source Beutler Lab
Gene Symbol Spc25
Ensembl Gene ENSMUSG00000005233
Gene Name SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)
Synonyms 2600017H08Rik, 2610205L13Rik, Spbc25
MMRRC Submission 044434-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.964) question?
Stock # R6242 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 69024239-69036538 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 69027555 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 112 (F112L)
Ref Sequence ENSEMBL: ENSMUSP00000128039 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005365] [ENSMUST00000112320] [ENSMUST00000127243] [ENSMUST00000149045] [ENSMUST00000149643] [ENSMUST00000167875]
AlphaFold Q3UA16
Predicted Effect probably damaging
Transcript: ENSMUST00000005365
AA Change: F160L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000005365
Gene: ENSMUSG00000005233
AA Change: F160L

DomainStartEndE-ValueType
low complexity region 46 57 N/A INTRINSIC
Pfam:Spindle_Spc25 148 222 6.3e-27 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000112320
AA Change: F160L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000107939
Gene: ENSMUSG00000005233
AA Change: F160L

DomainStartEndE-ValueType
low complexity region 46 57 N/A INTRINSIC
Pfam:Spindle_Spc25 150 221 1.3e-23 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126638
Predicted Effect probably damaging
Transcript: ENSMUST00000127243
AA Change: F145L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000120142
Gene: ENSMUSG00000005233
AA Change: F145L

DomainStartEndE-ValueType
low complexity region 1 12 N/A INTRINSIC
low complexity region 30 44 N/A INTRINSIC
coiled coil region 57 113 N/A INTRINSIC
Pfam:Spindle_Spc25 133 207 4.5e-24 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000149045
AA Change: F112L

PolyPhen 2 Score 0.298 (Sensitivity: 0.91; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000120999
Gene: ENSMUSG00000005233
AA Change: F112L

DomainStartEndE-ValueType
Pfam:Spindle_Spc25 100 133 3.7e-10 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149401
Predicted Effect probably damaging
Transcript: ENSMUST00000149643
AA Change: F160L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000117415
Gene: ENSMUSG00000005233
AA Change: F160L

DomainStartEndE-ValueType
low complexity region 46 57 N/A INTRINSIC
PDB:3IZ0|E 99 167 3e-22 PDB
Predicted Effect probably damaging
Transcript: ENSMUST00000167875
AA Change: F112L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000128039
Gene: ENSMUSG00000005233
AA Change: F112L

DomainStartEndE-ValueType
Pfam:Spindle_Spc25 100 174 1.7e-27 PFAM
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.5%
  • 20x: 95.9%
Validation Efficiency 99% (75/76)
MGI Phenotype FUNCTION: This gene encodes a component of the kinetochore-associated NDC80 protein complex, which is required for the mitotic spindle checkpoint and for microtubule-kinetochore attachment. During meiosis in mouse, the protein localizes to the germinal vesicle and then is associated with the chromosomes following germinal vesicle breakdown. Knockdown of this gene in oocytes results in precocious polar body extrusion, chromosome misalignment and aberrant spindle formation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
Allele List at MGI
Other mutations in this stock
Total: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adcy6 G T 15: 98,501,896 (GRCm39) C239* probably null Het
Akr1c6 A G 13: 4,486,361 (GRCm39) Q56R probably benign Het
Apaf1 T A 10: 90,898,025 (GRCm39) D244V probably damaging Het
Araf G T X: 20,726,339 (GRCm39) R601L probably damaging Homo
Arhgef11 C A 3: 87,635,385 (GRCm39) A898E probably benign Het
Asxl3 A T 18: 22,655,433 (GRCm39) N1148Y probably damaging Het
Atf6 T A 1: 170,621,545 (GRCm39) Q492L possibly damaging Het
Atrnl1 G T 19: 57,630,910 (GRCm39) V226F probably benign Het
Cfap68 C T 9: 50,675,215 (GRCm39) E148K probably benign Het
Cntnap1 A T 11: 101,073,364 (GRCm39) Y615F probably damaging Het
Crybg3 T C 16: 59,376,053 (GRCm39) T1734A probably benign Het
Ctdp1 A C 18: 80,502,427 (GRCm39) V161G probably damaging Het
Cyp4a30b T A 4: 115,311,587 (GRCm39) V85E possibly damaging Het
Dnase1l1 C T X: 73,320,644 (GRCm39) probably null Homo
Epha6 A T 16: 59,503,025 (GRCm39) W961R probably damaging Het
Fam114a1 A G 5: 65,188,695 (GRCm39) E475G probably damaging Het
Fam186a A G 15: 99,837,788 (GRCm39) Y2819H unknown Het
Fancm A T 12: 65,163,216 (GRCm39) Q1460L probably benign Het
Fancm C A 12: 65,163,223 (GRCm39) N1462K probably benign Het
Fgf14 T C 14: 124,913,940 (GRCm39) K64E probably benign Het
Fndc5 T C 4: 129,033,688 (GRCm39) V152A probably benign Het
Garem1 C G 18: 21,262,229 (GRCm39) V862L possibly damaging Het
Grin3b G A 10: 79,812,013 (GRCm39) G814R probably damaging Het
Hacd4 A G 4: 88,332,524 (GRCm39) S226P probably benign Het
Htt A G 5: 35,003,356 (GRCm39) Y1277C probably damaging Het
Igkv1-131 T A 6: 67,743,062 (GRCm39) D107V probably damaging Het
Iqcc T C 4: 129,510,639 (GRCm39) D292G probably damaging Het
Krtap13 C T 16: 88,548,384 (GRCm39) V35I probably damaging Het
Liat1 T C 11: 75,890,981 (GRCm39) S32P probably damaging Het
Lrrc59 G T 11: 94,525,809 (GRCm39) L132F possibly damaging Het
Mcub T C 3: 129,709,444 (GRCm39) S290G probably benign Het
Mettl4 A G 17: 95,042,802 (GRCm39) W345R probably damaging Het
Msgn1 G A 12: 11,258,526 (GRCm39) R142W probably damaging Het
Myo5c A G 9: 75,180,893 (GRCm39) I761V probably benign Het
Neb T A 2: 52,066,824 (GRCm39) K5879M probably damaging Het
Nkd2 C T 13: 73,970,905 (GRCm39) V226M probably damaging Het
Nt5el T A 13: 105,246,048 (GRCm39) V203E probably benign Het
Or51a24 T G 7: 103,733,771 (GRCm39) H172P possibly damaging Het
Or5b106 T A 19: 13,123,450 (GRCm39) H191L probably benign Het
Parp4 T A 14: 56,832,856 (GRCm39) L393* probably null Het
Pcdhgb6 G A 18: 37,876,608 (GRCm39) V439I probably benign Het
Pde1a T A 2: 79,959,136 (GRCm39) T15S probably benign Het
Pgr T A 9: 8,900,980 (GRCm39) I171N probably benign Het
Podxl T A 6: 31,503,180 (GRCm39) D296V probably benign Het
Polr3e A T 7: 120,539,690 (GRCm39) E479V possibly damaging Het
Prdm10 A T 9: 31,252,548 (GRCm39) H427L possibly damaging Het
Prl5a1 A T 13: 28,326,538 (GRCm39) K5* probably null Het
Prph A G 15: 98,955,004 (GRCm39) S325G probably damaging Het
Rabl2 C A 15: 89,468,555 (GRCm39) W49L probably benign Het
Rbbp8nl T A 2: 179,922,767 (GRCm39) I209F probably damaging Het
Rsf1 ATGGCG ATGGCGACGGTGGCG 7: 97,229,111 (GRCm39) probably benign Homo
Scn7a T C 2: 66,531,110 (GRCm39) D589G probably benign Het
Sdr42e1 A T 8: 118,389,936 (GRCm39) L235Q possibly damaging Het
Serpina3a T C 12: 104,082,260 (GRCm39) M11T probably benign Het
Slc6a4 A T 11: 76,909,184 (GRCm39) K399* probably null Het
Slco4c1 T A 1: 96,767,008 (GRCm39) T337S probably damaging Het
Swt1 A G 1: 151,283,365 (GRCm39) S331P probably benign Het
Tab1 A T 15: 80,039,971 (GRCm39) K264* probably null Het
Tagln3 T A 16: 45,544,701 (GRCm39) probably benign Het
Tbc1d2 C T 4: 46,629,912 (GRCm39) G252R probably benign Het
Tbck A G 3: 132,400,189 (GRCm39) D80G probably benign Het
Tcim A T 8: 24,928,911 (GRCm39) M1K probably null Het
Thap2 A G 10: 115,208,831 (GRCm39) S37P unknown Het
Tjp2 A T 19: 24,076,967 (GRCm39) probably null Het
Tln1 G A 4: 43,533,145 (GRCm39) S2390L probably damaging Het
Trpm5 T G 7: 142,626,919 (GRCm39) I1101L probably benign Het
Ttc3 T G 16: 94,243,554 (GRCm39) M831R probably benign Het
Tulp3 A G 6: 128,300,050 (GRCm39) C459R probably damaging Het
Uaca G A 9: 60,777,326 (GRCm39) R571Q probably damaging Het
Unc13b A T 4: 43,165,800 (GRCm39) T195S possibly damaging Het
Urgcp A G 11: 5,666,691 (GRCm39) L549P probably benign Het
Usp10 G T 8: 120,668,577 (GRCm39) A293S probably benign Het
Vmn2r23 A G 6: 123,681,359 (GRCm39) E89G possibly damaging Het
Vmn2r75 A C 7: 85,814,592 (GRCm39) D300E probably damaging Het
Wif1 T C 10: 120,870,366 (GRCm39) I40T possibly damaging Het
Zmynd8 G A 2: 165,740,867 (GRCm39) R6C possibly damaging Het
Other mutations in Spc25
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01757:Spc25 APN 2 69,032,952 (GRCm39) nonsense probably null
IGL02273:Spc25 APN 2 69,035,273 (GRCm39) splice site probably benign
IGL03163:Spc25 APN 2 69,027,548 (GRCm39) missense probably damaging 1.00
R1519:Spc25 UTSW 2 69,030,431 (GRCm39) missense probably damaging 1.00
R1604:Spc25 UTSW 2 69,035,498 (GRCm39) missense probably damaging 0.99
R2913:Spc25 UTSW 2 69,030,331 (GRCm39) missense probably benign 0.42
R3973:Spc25 UTSW 2 69,032,945 (GRCm39) missense probably damaging 1.00
R4094:Spc25 UTSW 2 69,032,975 (GRCm39) missense probably damaging 1.00
R4444:Spc25 UTSW 2 69,035,220 (GRCm39) missense probably benign 0.06
R5293:Spc25 UTSW 2 69,032,996 (GRCm39) missense possibly damaging 0.92
R6433:Spc25 UTSW 2 69,036,446 (GRCm39) utr 5 prime probably benign
R6721:Spc25 UTSW 2 69,027,517 (GRCm39) missense possibly damaging 0.96
R7712:Spc25 UTSW 2 69,036,481 (GRCm39) missense unknown
R7866:Spc25 UTSW 2 69,036,406 (GRCm39) critical splice donor site probably null
R8054:Spc25 UTSW 2 69,035,257 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGTGGCAAAATTACACTCTCAGCC -3'
(R):5'- TACTTATCAAAGATGGGGTGGG -3'

Sequencing Primer
(F):5'- ACACTCTCAGCCTTTAGAGGTCG -3'
(R):5'- ATCAAAGATGGGGTGGGGTGTG -3'
Posted On 2018-02-28