Mutagenetix > Incidental Mutation

Incidental Mutation 'R1468:Sycp3'

197736

Institutional Source

Beutler Lab

Gene Symbol

Sycp3

Ensembl Gene

ENSMUSG00000020059

Gene Name

synaptonemal complex protein 3

Synonyms

Scp3, Cor1

MMRRC Submission

039521-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.117) question?

Stock #

R1468 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

88295449-88309098 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 88305454 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 185 (V185A)

Ref Sequence

ENSEMBL: ENSMUSP00000020252 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020252] [ENSMUST00000020253] [ENSMUST00000117440] [ENSMUST00000123244] [ENSMUST00000125612] [ENSMUST00000126074] [ENSMUST00000139109] [ENSMUST00000148899]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000020252
AA Change: V185A

PolyPhen 2 Score 0.745 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000020252
Gene: ENSMUSG00000020059
AA Change: V185A

Domain	Start	End	E-Value	Type
low complexity region	42	53	N/A	INTRINSIC
Pfam:Cor1	101	229	6.1e-57	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000020253

SMART Domains

Protein: ENSMUSP00000020253
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
low complexity region	2	12	N/A	INTRINSIC
Pfam:CDP-OH_P_transf	59	183	1e-24	PFAM
transmembrane domain	191	213	N/A	INTRINSIC
transmembrane domain	226	248	N/A	INTRINSIC
transmembrane domain	263	282	N/A	INTRINSIC
transmembrane domain	295	317	N/A	INTRINSIC
transmembrane domain	349	371	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000117440

SMART Domains

Protein: ENSMUSP00000112708
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
low complexity region	2	12	N/A	INTRINSIC
Pfam:CDP-OH_P_transf	61	136	8.8e-18	PFAM
transmembrane domain	159	181	N/A	INTRINSIC
transmembrane domain	191	213	N/A	INTRINSIC
transmembrane domain	226	248	N/A	INTRINSIC
transmembrane domain	263	282	N/A	INTRINSIC
transmembrane domain	295	317	N/A	INTRINSIC
transmembrane domain	349	371	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000123244

SMART Domains

Protein: ENSMUSP00000137704
Gene: ENSMUSG00000020059

Domain	Start	End	E-Value	Type
low complexity region	42	53	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000125612
AA Change: V185A

PolyPhen 2 Score 0.520 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000137800
Gene: ENSMUSG00000020059
AA Change: V185A

Domain	Start	End	E-Value	Type
low complexity region	42	53	N/A	INTRINSIC
Pfam:Cor1	100	229	7.6e-60	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000126074

SMART Domains

Protein: ENSMUSP00000123429
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
low complexity region	2	12	N/A	INTRINSIC
Pfam:CDP-OH_P_transf	59	206	1.7e-24	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000134318

SMART Domains

Protein: ENSMUSP00000122428
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
transmembrane domain	20	42	N/A	INTRINSIC
transmembrane domain	55	77	N/A	INTRINSIC
transmembrane domain	109	131	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000139109

SMART Domains

Protein: ENSMUSP00000116413
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
low complexity region	2	12	N/A	INTRINSIC
Pfam:CDP-OH_P_transf	59	183	1e-24	PFAM
transmembrane domain	191	213	N/A	INTRINSIC
transmembrane domain	226	248	N/A	INTRINSIC
transmembrane domain	263	282	N/A	INTRINSIC
transmembrane domain	295	317	N/A	INTRINSIC
transmembrane domain	349	371	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000148899

SMART Domains

Protein: ENSMUSP00000120167
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
transmembrane domain	25	47	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000143108

SMART Domains

Protein: ENSMUSP00000117620
Gene: ENSMUSG00000060002

Domain	Start	End	E-Value	Type
Pfam:CDP-OH_P_transf	27	102	1.9e-18	PFAM
transmembrane domain	125	147	N/A	INTRINSIC
transmembrane domain	157	179	N/A	INTRINSIC

Meta Mutation Damage Score

0.0930

Coding Region Coverage

1x: 97.4%
3x: 96.7%
10x: 94.6%
20x: 90.1%

Validation Efficiency

98% (106/108)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an essential structural component of the synaptonemal complex. This complex is involved in synapsis, recombination and segregation of meiotic chromosomes. Mutations in this gene are associated with azoospermia in males and susceptibility to pregnancy loss in females. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2010]
PHENOTYPE: Homozygous mutants are male infertile and female sub-fertile. Reduced litter size in females is due to achiasmatic oocytes, resulting in aneuploidy and embryonic death. Meiosis in males blocks at early prophase with lack of synaptonemal complexes. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 112 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900092C05Rik	T	G	7: 12,246,507 (GRCm39)	M1R	probably null	Het
4933440N22Rik	C	A	6: 117,884,540 (GRCm39)		probably benign	Het
5031439G07Rik	G	T	15: 84,837,345 (GRCm39)	P280T	probably damaging	Het
Abca2	C	T	2: 25,331,308 (GRCm39)	S1267L	probably damaging	Het
Acsl3	A	T	1: 78,684,126 (GRCm39)	R719S	probably benign	Het
Adam1a	A	T	5: 121,657,839 (GRCm39)		probably null	Het
Adamts7	T	C	9: 90,070,851 (GRCm39)		probably benign	Het
Adgrf3	G	A	5: 30,407,227 (GRCm39)		probably benign	Het
Aldh6a1	T	C	12: 84,488,544 (GRCm39)	E89G	possibly damaging	Het
Ankrd36	A	G	11: 5,525,752 (GRCm39)	Y238C	probably damaging	Het
Ankrd65	G	A	4: 155,877,362 (GRCm39)	R291Q	probably benign	Het
Ano2	C	T	6: 125,773,227 (GRCm39)	R287W	probably damaging	Het
Ap1ar	A	G	3: 127,606,215 (GRCm39)	I125T	probably benign	Het
Arid1b	A	G	17: 5,293,197 (GRCm39)	D705G	probably damaging	Het
Asb18	T	A	1: 89,924,005 (GRCm39)	N86I	probably damaging	Het
Bicral	A	T	17: 47,135,519 (GRCm39)	S564T	probably benign	Het
Bpifa6	A	G	2: 153,831,192 (GRCm39)	M253V	probably benign	Het
Braf	T	C	6: 39,642,017 (GRCm39)	D194G	probably damaging	Het
Brinp3	C	A	1: 146,777,700 (GRCm39)	P716T	probably benign	Het
C7	T	A	15: 5,041,631 (GRCm39)	Y425F	probably damaging	Het
Ccdc102a	T	C	8: 95,632,714 (GRCm39)	K421R	probably benign	Het
Cep89	G	A	7: 35,120,388 (GRCm39)		probably null	Het
Chgb	A	T	2: 132,634,720 (GRCm39)	M221L	probably benign	Het
Chst14	A	G	2: 118,758,145 (GRCm39)	Y313C	probably damaging	Het
Ciita	G	A	16: 10,331,152 (GRCm39)		probably null	Het
Clec12b	A	T	6: 129,357,603 (GRCm39)	I85N	probably damaging	Het
Clec2e	G	T	6: 129,070,459 (GRCm39)	Y187*	probably null	Het
Crbn	T	C	6: 106,767,804 (GRCm39)	K229E	probably benign	Het
Ctdspl2	A	T	2: 121,811,762 (GRCm39)	Q201L	probably benign	Het
Ctrb1	G	T	8: 112,416,041 (GRCm39)		probably benign	Het
Cyp2c55	T	A	19: 38,999,525 (GRCm39)	V77E	probably damaging	Het
Cyp2c69	A	C	19: 39,837,839 (GRCm39)	D414E	probably damaging	Het
Ddx47	T	C	6: 134,988,703 (GRCm39)		probably benign	Het
Dlg1	A	G	16: 31,661,640 (GRCm39)		probably null	Het
Dnah5	C	A	15: 28,230,609 (GRCm39)	S169*	probably null	Het
Dock4	C	A	12: 40,805,809 (GRCm39)	T927K	probably benign	Het
Esrp2	T	G	8: 106,860,453 (GRCm39)	D259A	probably damaging	Het
Fam169a	A	G	13: 97,255,038 (GRCm39)	K418R	probably benign	Het
Fancm	A	T	12: 65,146,067 (GRCm39)	I597F	probably damaging	Het
Fastkd2	G	T	1: 63,771,385 (GRCm39)		probably benign	Het
Fat1	G	A	8: 45,463,582 (GRCm39)	V1375M	probably damaging	Het
Fbxw10	A	T	11: 62,753,464 (GRCm39)	D486V	probably damaging	Het
Fech	C	T	18: 64,603,744 (GRCm39)		probably benign	Het
Fermt1	C	T	2: 132,766,942 (GRCm39)	E342K	probably benign	Het
Foxp1	T	A	6: 98,955,181 (GRCm39)	H195L	possibly damaging	Het
Gfra1	T	A	19: 58,440,407 (GRCm39)	I138L	probably benign	Het
Gm12185	T	C	11: 48,806,501 (GRCm39)	D230G	possibly damaging	Het
Gm14403	T	A	2: 177,199,024 (GRCm39)		probably benign	Het
Gpd2	A	C	2: 57,245,786 (GRCm39)	T439P	probably damaging	Het
Gpm6a	A	T	8: 55,490,385 (GRCm39)	K20N	probably damaging	Het
Hc	A	T	2: 34,873,819 (GRCm39)	Y158*	probably null	Het
Hectd4	A	T	5: 121,487,235 (GRCm39)	D3410V	possibly damaging	Het
Il17b	G	A	18: 61,823,483 (GRCm39)		probably null	Het
Irx4	G	T	13: 73,413,695 (GRCm39)	R55L	possibly damaging	Het
Itgav	A	T	2: 83,596,245 (GRCm39)		probably benign	Het
Lama3	T	C	18: 12,574,164 (GRCm39)	V582A	probably benign	Het
Ldhd	G	T	8: 112,353,925 (GRCm39)	A425E	possibly damaging	Het
Lrp1b	C	T	2: 40,817,841 (GRCm39)		probably null	Het
Lrp5	T	C	19: 3,670,191 (GRCm39)	T638A	possibly damaging	Het
Lrrk1	A	C	7: 65,909,722 (GRCm39)	F1996C	probably damaging	Het
Ly6h	G	A	15: 75,437,986 (GRCm39)	S21L	probably benign	Het
Mctp1	T	C	13: 76,973,392 (GRCm39)	V431A	probably benign	Het
Metap2	C	T	10: 93,707,345 (GRCm39)		probably null	Het
Mfsd2b	T	A	12: 4,920,536 (GRCm39)	K94*	probably null	Het
Micall2	A	G	5: 139,705,097 (GRCm39)	L79P	probably damaging	Het
Mucl2	T	C	15: 103,927,673 (GRCm39)	T95A	possibly damaging	Het
Myo15a	A	T	11: 60,396,832 (GRCm39)	T2634S	probably damaging	Het
Myo5b	G	T	18: 74,873,574 (GRCm39)	V1467L	probably damaging	Het
Nfic	G	T	10: 81,256,414 (GRCm39)	D105E	probably damaging	Het
Nrdc	T	A	4: 108,873,865 (GRCm39)	F227Y	probably benign	Het
Nrp2	A	T	1: 62,777,458 (GRCm39)	I88F	probably damaging	Het
Nup160	A	T	2: 90,530,887 (GRCm39)	H515L	probably benign	Het
Nup205	G	A	6: 35,202,917 (GRCm39)		probably null	Het
Oas1g	G	A	5: 121,020,069 (GRCm39)	T179I	probably benign	Het
Ogfr	A	T	2: 180,236,543 (GRCm39)	E376V	probably damaging	Het
Or2l13	T	G	16: 19,306,378 (GRCm39)	S263R	probably benign	Het
Or4a69	A	T	2: 89,312,855 (GRCm39)	V208D	possibly damaging	Het
Or4c107	T	G	2: 88,789,387 (GRCm39)	Y192*	probably null	Het
Or52d1	G	T	7: 103,755,896 (GRCm39)	V137F	possibly damaging	Het
Or5p6	C	T	7: 107,631,595 (GRCm39)		probably null	Het
Pard3b	T	C	1: 62,384,188 (GRCm39)	V851A	probably benign	Het
Pcdhb16	A	T	18: 37,611,142 (GRCm39)	Y34F	probably damaging	Het
Pikfyve	T	C	1: 65,290,825 (GRCm39)	Y1215H	probably damaging	Het
Pkhd1	A	T	1: 20,593,565 (GRCm39)	V1516E	probably damaging	Het
Pla2g4a	A	T	1: 149,763,344 (GRCm39)		probably benign	Het
Ptprg	A	T	14: 12,190,767 (GRCm38)	I818F	probably benign	Het
Ralgapb	A	G	2: 158,304,173 (GRCm39)	E644G	possibly damaging	Het
Rbm45	A	G	2: 76,202,459 (GRCm39)	I127M	probably damaging	Het
Rtp2	T	C	16: 23,746,220 (GRCm39)	Y157C	probably damaging	Het
Sema3f	A	T	9: 107,564,771 (GRCm39)		probably benign	Het
Sf3b3	A	T	8: 111,564,006 (GRCm39)	Y329N	probably damaging	Het
Sfxn1	A	G	13: 54,239,646 (GRCm39)		probably null	Het
Shkbp1	A	T	7: 27,044,751 (GRCm39)	C447S	probably damaging	Het
Sipa1l3	A	G	7: 29,021,685 (GRCm39)	S689P	possibly damaging	Het
Slc7a8	A	G	14: 54,970,656 (GRCm39)	S332P	probably damaging	Het
Slit1	C	A	19: 41,596,823 (GRCm39)	C1092F	probably damaging	Het
Slx9	A	G	10: 77,333,360 (GRCm39)		probably benign	Het
Stard9	A	G	2: 120,533,678 (GRCm39)	I619V	possibly damaging	Het
Taar9	A	T	10: 23,985,382 (GRCm39)	N17K	possibly damaging	Het
Tbkbp1	T	C	11: 97,039,814 (GRCm39)	E102G	probably damaging	Het
Tex44	A	G	1: 86,354,834 (GRCm39)	N248D	probably benign	Het
Tmem63b	C	G	17: 45,989,904 (GRCm39)	R88P	possibly damaging	Het
Tnpo1	C	T	13: 98,986,665 (GRCm39)	V781I	probably benign	Het
Tonsl	C	T	15: 76,520,761 (GRCm39)		probably null	Het
Ttc6	A	G	12: 57,721,463 (GRCm39)	K984R	possibly damaging	Het
Usp34	A	G	11: 23,391,171 (GRCm39)	E2263G	probably damaging	Het
Usp8	A	G	2: 126,596,847 (GRCm39)	K875E	probably damaging	Het
Vapb	C	T	2: 173,603,905 (GRCm39)		probably benign	Het
Vmn1r223	A	G	13: 23,434,038 (GRCm39)	I211V	possibly damaging	Het
Vmn2r81	G	A	10: 79,129,496 (GRCm39)	V796I	probably damaging	Het
Wdr90	A	T	17: 26,073,027 (GRCm39)	V856D	probably damaging	Het
Wnk2	T	A	13: 49,235,571 (GRCm39)	T615S	probably damaging	Het

Other mutations in Sycp3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02103:Sycp3	APN	10	88,302,334 (GRCm39)	missense	possibly damaging	0.65
IGL02402:Sycp3	APN	10	88,302,425 (GRCm39)	intron	probably benign
PIT4378001:Sycp3	UTSW	10	88,302,366 (GRCm39)	nonsense	probably null
R1468:Sycp3	UTSW	10	88,305,454 (GRCm39)	missense	possibly damaging	0.75
R2857:Sycp3	UTSW	10	88,303,234 (GRCm39)	missense	probably damaging	1.00
R2858:Sycp3	UTSW	10	88,303,234 (GRCm39)	missense	probably damaging	1.00
R2897:Sycp3	UTSW	10	88,308,544 (GRCm39)	missense	possibly damaging	0.92
R2898:Sycp3	UTSW	10	88,308,544 (GRCm39)	missense	possibly damaging	0.92
R4194:Sycp3	UTSW	10	88,299,237 (GRCm39)	missense	probably benign	0.01
R5683:Sycp3	UTSW	10	88,308,797 (GRCm39)	missense	probably damaging	1.00
R6882:Sycp3	UTSW	10	88,308,791 (GRCm39)	nonsense	probably null
R7273:Sycp3	UTSW	10	88,305,428 (GRCm39)	missense	probably damaging	1.00
R7853:Sycp3	UTSW	10	88,302,368 (GRCm39)	missense	probably damaging	1.00
R8055:Sycp3	UTSW	10	88,298,438 (GRCm39)	missense	probably damaging	1.00
R8147:Sycp3	UTSW	10	88,298,467 (GRCm39)	critical splice donor site	probably null
R8720:Sycp3	UTSW	10	88,298,394 (GRCm39)	missense	probably benign	0.38
R8872:Sycp3	UTSW	10	88,302,388 (GRCm39)	missense	probably damaging	1.00
R9163:Sycp3	UTSW	10	88,299,734 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- CAGAGGCAGGCATTGGTTGAATATACA -3'
(R):5'- GAACATATCTTAggggcaagagatggc -3'

Sequencing Primer
(F):5'- gctgagagcctggattatagaaac -3'
(R):5'- ctactacccttttctgacctctg -3'

Posted On

2014-05-23