Mutagenetix > Incidental Mutation

Incidental Mutation 'R1519:Spc25'

167245

Institutional Source

Beutler Lab

Gene Symbol

Spc25

Ensembl Gene

ENSMUSG00000005233

Gene Name

SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)

Synonyms

2600017H08Rik, Spbc25, 2610205L13Rik

Accession Numbers

Essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R1519 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

69193895-69206194 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 69200087 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 71 (I71V)

Ref Sequence

ENSEMBL: ENSMUSP00000120999 (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: I119V

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000005365
Gene: ENSMUSG00000005233
AA Change: I119V

Domain	Start	End	E-Value	Type
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: I119V

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000107939
Gene: ENSMUSG00000005233
AA Change: I119V

Domain	Start	End	E-Value	Type
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

possibly damaging
Transcript: ENSMUST00000127243
AA Change: I104V

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000120142
Gene: ENSMUSG00000005233
AA Change: I104V

Domain	Start	End	E-Value	Type
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 damaging
Transcript: ENSMUST00000149045
AA Change: I71V

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000120999
Gene: ENSMUSG00000005233
AA Change: I71V

Domain	Start	End	E-Value	Type
Pfam:Spindle_Spc25	100	133	3.7e-10	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149401

Predicted Effect

probably damaging
Transcript: ENSMUST00000149643
AA Change: I119V

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000117415
Gene: ENSMUSG00000005233
AA Change: I119V

Domain	Start	End	E-Value	Type
low complexity region	46	57	N/A	INTRINSIC
PDB:3IZ0\|E	99	167	3e-22	PDB

Predicted Effect

probably damaging
Transcript: ENSMUST00000167875
AA Change: I71V

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000128039
Gene: ENSMUSG00000005233
AA Change: I71V

Domain	Start	End	E-Value	Type
Pfam:Spindle_Spc25	100	174	1.7e-27	PFAM

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 92.9%

Validation Efficiency

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017N19Rik	C	G	10: 100,603,528 (GRCm38)	P187R	probably damaging	Het
9230019H11Rik	A	G	10: 3,125,230 (GRCm38)		noncoding transcript	Het
9530077C05Rik	T	G	9: 22,430,375 (GRCm38)	L114R	probably benign	Het
Abhd5	T	C	9: 122,379,014 (GRCm38)		probably null	Het
Acadvl	A	G	11: 70,014,791 (GRCm38)		probably null	Het
Actn1	T	C	12: 80,205,078 (GRCm38)	E75G	probably damaging	Het
Adam4	A	T	12: 81,420,877 (GRCm38)	N323K	possibly damaging	Het
Anks6	G	A	4: 47,027,152 (GRCm38)	R689W	probably damaging	Het
Anxa2	T	C	9: 69,485,241 (GRCm38)	I124T	probably damaging	Het
Aph1c	T	C	9: 66,833,265 (GRCm38)	T10A	probably benign	Het
Arhgap40	T	A	2: 158,546,801 (GRCm38)	W552R	probably benign	Het
Baz2b	C	T	2: 59,948,254 (GRCm38)	R754H	possibly damaging	Het
Blmh	A	G	11: 76,966,781 (GRCm38)	Y147C	probably damaging	Het
C1galt1	C	T	6: 7,866,402 (GRCm38)	L83F	probably damaging	Het
Cd163l1	G	A	7: 140,228,156 (GRCm38)	V747I	probably benign	Het
Cdh23	A	T	10: 60,379,343 (GRCm38)	Y1403N	possibly damaging	Het
Cic	A	T	7: 25,293,810 (GRCm38)		probably null	Het
Coro1b	T	A	19: 4,150,584 (GRCm38)	V200D	possibly damaging	Het
Csl	T	A	10: 99,757,955 (GRCm38)	E416V	probably damaging	Het
Cyp3a25	A	G	5: 146,001,447 (GRCm38)		probably null	Het
Dennd2d	T	A	3: 106,492,559 (GRCm38)	F266Y	probably damaging	Het
Dnah10	A	G	5: 124,760,952 (GRCm38)	E1072G	probably damaging	Het
Dnah6	T	A	6: 73,049,048 (GRCm38)	K3435N	probably damaging	Het
Dnah9	G	A	11: 65,881,761 (GRCm38)	A3715V	probably damaging	Het
Fam186a	G	A	15: 99,947,655 (GRCm38)	S236L	unknown	Het
Fam198b	A	G	3: 79,941,464 (GRCm38)	N506D	possibly damaging	Het
Frs3	A	G	17: 47,702,978 (GRCm38)	T199A	probably benign	Het
Fsd1	A	G	17: 55,993,870 (GRCm38)	N243S	probably benign	Het
Gabra5	A	C	7: 57,408,893 (GRCm38)	L369R	probably benign	Het
Gins4	A	G	8: 23,234,776 (GRCm38)	V54A	probably benign	Het
Gli1	T	C	10: 127,334,269 (GRCm38)	E339G	possibly damaging	Het
Gm12185	A	G	11: 48,907,767 (GRCm38)	V633A	probably damaging	Het
Gm8251	A	G	1: 44,056,970 (GRCm38)	V1656A	probably benign	Het
Gm8765	G	A	13: 50,700,407 (GRCm38)		probably null	Het
Gpr83	T	A	9: 14,868,197 (GRCm38)	C182S	probably null	Het
Gspt1	A	G	16: 11,220,855 (GRCm38)	V627A	probably damaging	Het
Heatr1	T	C	13: 12,412,159 (GRCm38)	C722R	probably benign	Het
Jak1	C	T	4: 101,162,922 (GRCm38)	R680Q	probably damaging	Het
Kif2c	A	G	4: 117,169,940 (GRCm38)	V287A	probably damaging	Het
Kmo	A	G	1: 175,656,802 (GRCm38)	E366G	probably damaging	Het
Kmo	C	T	1: 175,651,618 (GRCm38)	P240L	possibly damaging	Het
Lepr	A	T	4: 101,789,344 (GRCm38)	N824I	probably damaging	Het
Lyrm7	T	A	11: 54,848,599 (GRCm38)	H75L	possibly damaging	Het
Map4k1	A	T	7: 28,991,036 (GRCm38)	Q351L	probably benign	Het
Mgam	T	C	6: 40,661,683 (GRCm38)	I450T	probably benign	Het
Nbeal2	A	G	9: 110,636,305 (GRCm38)	L955P	probably damaging	Het
Nlrp9c	T	C	7: 26,378,101 (GRCm38)	K752R	possibly damaging	Het
Nsmaf	A	T	4: 6,438,062 (GRCm38)	I70K	probably benign	Het
Olfr201	C	T	16: 59,268,944 (GRCm38)	C241Y	probably damaging	Het
Olfr298	A	G	7: 86,489,125 (GRCm38)	M142T	probably damaging	Het
Otud7a	A	G	7: 63,758,643 (GRCm38)	Y898C	probably damaging	Het
Pcdhb18	A	C	18: 37,490,892 (GRCm38)	D425A	probably damaging	Het
Prdm1	A	T	10: 44,439,986 (GRCm38)	L733*	probably null	Het
Prdm2	A	T	4: 143,135,583 (GRCm38)	I379N	probably damaging	Het
Ptprg	A	T	14: 12,220,596 (GRCm38)	Y436F	probably damaging	Het
Riok3	A	G	18: 12,137,306 (GRCm38)	D167G	probably damaging	Het
Rnf215	G	T	11: 4,135,451 (GRCm38)	R60L	probably damaging	Het
Sdk1	A	T	5: 141,999,950 (GRCm38)	H779L	probably benign	Het
Serpine2	A	G	1: 79,795,031 (GRCm38)	F390L	probably damaging	Het
Sh3d21	T	A	4: 126,151,726 (GRCm38)	K387*	probably null	Het
Slc13a2	T	C	11: 78,397,746 (GRCm38)	Y568C	possibly damaging	Het
Slc27a5	T	C	7: 12,988,459 (GRCm38)		probably null	Het
Slc32a1	T	C	2: 158,614,577 (GRCm38)	L384P	probably damaging	Het
Sorcs1	T	C	19: 50,252,587 (GRCm38)	N454D	probably benign	Het
Spag8	T	C	4: 43,652,777 (GRCm38)	Y228C	possibly damaging	Het
Tcte1	T	A	17: 45,535,252 (GRCm38)	F261I	probably damaging	Het
Thsd7a	T	A	6: 12,471,175 (GRCm38)	K481N	probably benign	Het
Tll2	G	T	19: 41,086,400 (GRCm38)	N908K	probably benign	Het
Tmem236	T	C	2: 14,192,280 (GRCm38)	V93A	probably benign	Het
Top2b	G	A	14: 16,408,953 (GRCm38)		probably null	Het
Topaz1	G	A	9: 122,767,011 (GRCm38)	S949N	probably benign	Het
Triobp	A	G	15: 78,973,738 (GRCm38)	T1180A	probably benign	Het
Trip11	A	C	12: 101,886,160 (GRCm38)	D548E	probably benign	Het
Trpv2	T	A	11: 62,589,826 (GRCm38)		probably null	Het
Vmn1r12	T	A	6: 57,159,555 (GRCm38)	H212Q	probably damaging	Het
Vmn2r112	A	G	17: 22,618,903 (GRCm38)	T782A	possibly damaging	Het
Vmn2r7	A	G	3: 64,716,455 (GRCm38)	V239A	possibly damaging	Het
Vmn2r80	T	A	10: 79,194,219 (GRCm38)	N626K	probably damaging	Het
Vmn2r99	A	G	17: 19,380,060 (GRCm38)	S449G	probably benign	Het
Wfikkn2	T	C	11: 94,238,107 (GRCm38)	T403A	probably benign	Het
Xirp2	A	G	2: 67,515,679 (GRCm38)	I2755V	probably benign	Het
Yjefn3	A	G	8: 69,889,079 (GRCm38)	V153A	probably benign	Het
Zfp677	C	A	17: 21,397,237 (GRCm38)	H185Q	possibly damaging	Het
Zfp947	C	T	17: 22,146,292 (GRCm38)	V134I	probably benign	Het

Other mutations in Spc25

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01757:Spc25	APN	2	69,202,608 (GRCm38)	nonsense	probably null
IGL02273:Spc25	APN	2	69,204,929 (GRCm38)	splice site	probably benign
IGL03163:Spc25	APN	2	69,197,204 (GRCm38)	missense	probably damaging	1.00
R1604:Spc25	UTSW	2	69,205,154 (GRCm38)	missense	probably damaging	0.99
R2913:Spc25	UTSW	2	69,199,987 (GRCm38)	missense	probably benign	0.42
R3973:Spc25	UTSW	2	69,202,601 (GRCm38)	missense	probably damaging	1.00
R4094:Spc25	UTSW	2	69,202,631 (GRCm38)	missense	probably damaging	1.00
R4444:Spc25	UTSW	2	69,204,876 (GRCm38)	missense	probably benign	0.06
R5293:Spc25	UTSW	2	69,202,652 (GRCm38)	missense	possibly damaging	0.92
R6242:Spc25	UTSW	2	69,197,211 (GRCm38)	missense	probably damaging	1.00
R6433:Spc25	UTSW	2	69,206,102 (GRCm38)	utr 5 prime	probably benign
R6721:Spc25	UTSW	2	69,197,173 (GRCm38)	missense	possibly damaging	0.96
R7712:Spc25	UTSW	2	69,206,137 (GRCm38)	missense	unknown
R7866:Spc25	UTSW	2	69,206,062 (GRCm38)	critical splice donor site	probably null
R8054:Spc25	UTSW	2	69,204,913 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GAGTTCGATACAAATGCCAGTGAAAACC -3'
(R):5'- AGCAGTTGTAAACCAGCCTGAAATAAGG -3'

Sequencing Primer
(F):5'- GTCAAACTTTCATTAGACACTGGG -3'
(R):5'- GCAaacaacaataacaacaacaac -3'

Posted On

2014-04-13