Mutagenetix > Incidental Mutation

Incidental Mutation 'R3973:Spc25'

312922

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

040841-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R3973 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

69024239-69036538 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 69032945 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 60 (L60P)

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: L108P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000005365
Gene: ENSMUSG00000005233
AA Change: L108P

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: L108P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000107939
Gene: ENSMUSG00000005233
AA Change: L108P

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

probably damaging
Transcript: ENSMUST00000127243
AA Change: L93P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000120142
Gene: ENSMUSG00000005233
AA Change: L93P

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: L60P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000120999
Gene: ENSMUSG00000005233
AA Change: L60P

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: L108P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000117415
Gene: ENSMUSG00000005233
AA Change: L108P

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: L60P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000128039
Gene: ENSMUSG00000005233
AA Change: L60P

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150505

Meta Mutation Damage Score

0.6102

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.8%
20x: 93.3%

Validation Efficiency

98% (61/62)

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510039O18Rik	T	C	4: 148,029,488 (GRCm39)	I486T	probably damaging	Het
4933427D14Rik	T	C	11: 72,089,567 (GRCm39)	R106G	probably damaging	Het
Cfap54	A	G	10: 92,675,333 (GRCm39)	S2863P	possibly damaging	Het
Copa	T	A	1: 171,948,812 (GRCm39)	S1155T	probably benign	Het
Crot	T	C	5: 9,027,541 (GRCm39)	T264A	probably benign	Het
Ddx3y	G	A	Y: 1,267,170 (GRCm39)	A232V	probably damaging	Het
Dst	T	G	1: 34,050,979 (GRCm39)	V25G	probably benign	Het
Ehbp1	C	T	11: 22,087,867 (GRCm39)	A406T	probably benign	Het
Eml5	A	T	12: 98,768,724 (GRCm39)		probably benign	Het
Eps8	A	T	6: 137,486,153 (GRCm39)	M453K	probably benign	Het
Galnt3	T	C	2: 65,937,374 (GRCm39)	D112G	possibly damaging	Het
Glra4	C	T	X: 135,663,542 (GRCm39)	A336T	probably damaging	Het
Gmppb	A	G	9: 107,927,338 (GRCm39)	D95G	probably benign	Het
Gprc6a	T	C	10: 51,504,544 (GRCm39)	Y100C	possibly damaging	Het
Gpx6	C	A	13: 21,501,828 (GRCm39)	S150Y	probably damaging	Het
Hsd17b3	A	T	13: 64,207,300 (GRCm39)	V247D	probably damaging	Het
Htr7	T	C	19: 36,034,160 (GRCm39)	D165G	probably damaging	Het
Igha	T	C	12: 113,219,972 (GRCm39)		probably benign	Het
Igsf10	A	G	3: 59,239,345 (GRCm39)	C279R	probably damaging	Het
Irak4	A	G	15: 94,452,621 (GRCm39)	E182G	possibly damaging	Het
Lipo3	A	T	19: 33,535,723 (GRCm39)	V274E	probably damaging	Het
Lrpprc	A	C	17: 85,078,269 (GRCm39)		probably null	Het
Mast1	T	C	8: 85,645,393 (GRCm39)	Y684C	probably damaging	Het
Mdn1	T	C	4: 32,722,363 (GRCm39)	F2382L	probably benign	Het
Mepe	C	T	5: 104,484,944 (GRCm39)	P28L	probably benign	Het
Mrgpra3	T	A	7: 47,239,414 (GRCm39)	I171F	probably benign	Het
Muc2	T	A	7: 141,300,541 (GRCm39)		probably benign	Het
Myh3	C	T	11: 66,987,262 (GRCm39)	Q1371*	probably null	Het
Nodal	T	A	10: 61,258,833 (GRCm39)	V90E	probably benign	Het
Npas4	A	T	19: 5,036,579 (GRCm39)	H528Q	probably benign	Het
Nt5dc3	T	C	10: 86,660,100 (GRCm39)	V382A	probably damaging	Het
Pcdh18	G	A	3: 49,709,035 (GRCm39)	T293I	probably damaging	Het
Phf20l1	A	G	15: 66,513,665 (GRCm39)	D947G	probably damaging	Het
Phf8-ps	A	T	17: 33,285,405 (GRCm39)	S466T	probably benign	Het
Pla2r1	A	G	2: 60,279,306 (GRCm39)	V758A	probably benign	Het
Plod2	G	T	9: 92,480,672 (GRCm39)	G422*	probably null	Het
Ppp1r12a	T	C	10: 108,089,341 (GRCm39)	V660A	probably benign	Het
Prdm6	T	C	18: 53,673,278 (GRCm39)	I186T	possibly damaging	Het
Prkd3	G	A	17: 79,266,570 (GRCm39)		probably benign	Het
Prrc2a	A	G	17: 35,376,908 (GRCm39)	L734P	probably damaging	Het
Rnf128	C	A	X: 138,565,271 (GRCm39)	L282I	probably damaging	Het
Rnf213	A	G	11: 119,359,879 (GRCm39)	N4424S		Het
Scrn3	T	C	2: 73,166,121 (GRCm39)	S385P	possibly damaging	Het
Serpina1d	A	T	12: 103,734,107 (GRCm39)	S66T	probably benign	Het
Setd3	T	C	12: 108,131,417 (GRCm39)	K3R	possibly damaging	Het
Slc2a7	A	G	4: 150,242,667 (GRCm39)		probably null	Het
Smad4	G	T	18: 73,810,807 (GRCm39)	T59K	possibly damaging	Het
Stam	A	C	2: 14,143,772 (GRCm39)	H354P	probably damaging	Het
Tesk1	C	T	4: 43,445,786 (GRCm39)	P280S	possibly damaging	Het
Tmem120a	C	G	5: 135,765,131 (GRCm39)	R254P	probably benign	Het
Traf5	T	C	1: 191,729,837 (GRCm39)	T405A	probably benign	Het
Trav7-4	A	G	14: 53,699,119 (GRCm39)	S89G	probably benign	Het
Tsc22d1	T	C	14: 76,656,049 (GRCm39)	S761P	probably damaging	Het
Ugt1a10	C	A	1: 88,143,862 (GRCm39)	H361N	probably damaging	Het
Ugt2b1	C	A	5: 87,065,534 (GRCm39)	V502L	probably benign	Het
Vip	T	A	10: 5,592,590 (GRCm39)	S77T	possibly damaging	Het
Wdr72	A	T	9: 74,125,979 (GRCm39)	M1025L	probably benign	Het
Zfp541	A	G	7: 15,806,147 (GRCm39)	D94G	probably damaging	Het

Other mutations in Spc25

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
R6242:Spc25	UTSW	2	69,027,555 (GRCm39)	missense	probably damaging	1.00
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'- TTAAGTGATACCTAGAGAGATGCTGG -3'
(R):5'- TGTACTTGGAACTGAAGGAGTC -3'

Sequencing Primer
(F):5'- ATACCTAGAGAGATGCTGGTCTGTC -3'
(R):5'- GCCAAAGAATTGTGAGTTTCAGGTC -3'

Posted On

2015-04-30