Mutagenetix > Incidental Mutation

Incidental Mutation 'R2897:Sycp3'

260858

Institutional Source

Beutler Lab

Gene Symbol

Sycp3

Ensembl Gene

ENSMUSG00000020059

Gene Name

synaptonemal complex protein 3

Synonyms

Scp3, Cor1

MMRRC Submission

040485-MU

Accession Numbers

Essential gene?

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

Stock #

R2897 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

88295449-88309098 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 88308544 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Lysine at position 205 (E205K)

Ref Sequence

ENSEMBL: ENSMUSP00000137800 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000020252
AA Change: E205K

PolyPhen 2 Score 0.824 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000020252
Gene: ENSMUSG00000020059
AA Change: E205K

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: E205K

PolyPhen 2 Score 0.921 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000137800
Gene: ENSMUSG00000020059
AA Change: E205K

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: 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

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

Meta Mutation Damage Score

0.1659

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

99% (72/73)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	T	C	13: 77,471,640 (GRCm39)	V1015A	probably benign	Het
4930480E11Rik	C	T	X: 77,413,868 (GRCm39)	Q198*	probably null	Het
Acap3	G	C	4: 155,989,388 (GRCm39)		probably null	Het
Adamts14	T	C	10: 61,040,689 (GRCm39)	D879G	probably damaging	Het
Akap1	A	T	11: 88,735,605 (GRCm39)	C352*	probably null	Het
Ankk1	T	A	9: 49,333,122 (GRCm39)	T121S	probably benign	Het
Ankrd6	T	C	4: 32,860,438 (GRCm39)	S2G	probably damaging	Het
Anks1	G	T	17: 28,204,337 (GRCm39)		probably null	Het
Apob	G	A	12: 8,060,356 (GRCm39)	G2946D	probably damaging	Het
Atm	A	C	9: 53,419,105 (GRCm39)	C782W	probably damaging	Het
Atp1a4	A	T	1: 172,074,257 (GRCm39)	I332N	probably damaging	Het
Bnc2	T	C	4: 84,211,152 (GRCm39)	I406V	probably damaging	Het
Cdh20	A	T	1: 104,875,199 (GRCm39)	D327V	probably damaging	Het
Cep192	T	A	18: 67,988,341 (GRCm39)		probably null	Het
Chd5	T	C	4: 152,456,572 (GRCm39)	F970L	probably damaging	Het
Coq9	T	C	8: 95,579,752 (GRCm39)	Y236H	probably damaging	Het
Csn1s2a	A	G	5: 87,929,680 (GRCm39)	H93R	unknown	Het
Cxcr2	T	C	1: 74,198,130 (GRCm39)	V208A	probably benign	Het
Cyp1b1	G	A	17: 80,021,160 (GRCm39)	T194M	probably benign	Het
Dbt	T	A	3: 116,317,061 (GRCm39)	V79E	probably damaging	Het
Dcx	A	G	X: 142,706,428 (GRCm39)		probably benign	Het
Dnm3	G	A	1: 162,113,643 (GRCm39)		probably benign	Het
Erbin	C	T	13: 104,022,705 (GRCm39)	E45K	probably damaging	Het
Fastkd1	A	G	2: 69,532,960 (GRCm39)	L469P	probably damaging	Het
Gkn3	C	T	6: 87,360,507 (GRCm39)	A163T	probably damaging	Het
Gm10271	A	G	10: 116,808,495 (GRCm39)	L7S	probably damaging	Het
Gm5087	T	C	14: 13,158,805 (GRCm38)		noncoding transcript	Het
Hid1	A	G	11: 115,241,356 (GRCm39)	S645P	probably benign	Het
Hmcn1	C	T	1: 150,678,624 (GRCm39)	C499Y	probably damaging	Het
Ifna1	C	A	4: 88,768,450 (GRCm39)	Q43K	probably benign	Het
Ikbkb	G	T	8: 23,159,693 (GRCm39)	Q432K	possibly damaging	Het
Inpp4a	A	T	1: 37,405,675 (GRCm39)	H148L	probably benign	Het
Itpr2	C	T	6: 146,074,839 (GRCm39)	R2338Q	probably benign	Het
Itpr2	A	T	6: 146,224,667 (GRCm39)	I1441N	probably damaging	Het
Krt78	T	C	15: 101,855,541 (GRCm39)	R757G	probably benign	Het
Lmx1a	T	A	1: 167,658,109 (GRCm39)		probably benign	Het
Lpxn	T	A	19: 12,796,722 (GRCm39)	S81T	probably benign	Het
Lrriq1	T	C	10: 103,063,111 (GRCm39)	N65S	probably damaging	Het
Mis18bp1	T	C	12: 65,180,360 (GRCm39)	D981G	probably benign	Het
Mpp4	T	C	1: 59,183,853 (GRCm39)	I296V	probably benign	Het
Mtrf1l	T	C	10: 5,767,565 (GRCm39)	R184G	probably benign	Het
Muc19	T	C	15: 91,822,550 (GRCm39)		noncoding transcript	Het
Myo6	T	A	9: 80,176,893 (GRCm39)		probably null	Het
Myom1	A	G	17: 71,408,215 (GRCm39)		probably benign	Het
Ndrg4	A	G	8: 96,405,014 (GRCm39)		probably null	Het
Neu2	A	G	1: 87,522,782 (GRCm39)	S72G	probably benign	Het
Nlrc4	T	A	17: 74,755,040 (GRCm39)	M59L	probably benign	Het
Nuak2	A	T	1: 132,252,791 (GRCm39)	H115L	probably damaging	Het
Oog1	T	A	12: 87,655,178 (GRCm39)	I272K	probably damaging	Het
Or10aa1	T	C	1: 173,869,699 (GRCm39)	F61S	probably damaging	Het
Or52a20	A	T	7: 103,366,749 (GRCm39)	Y316F	probably benign	Het
Pcdhb1	A	G	18: 37,399,516 (GRCm39)	Y489C	probably damaging	Het
Pde5a	T	C	3: 122,572,651 (GRCm39)	I344T	probably benign	Het
Pip5kl1	C	A	2: 32,473,359 (GRCm39)	A332D	probably benign	Het
Pja1	T	C	X: 98,510,754 (GRCm39)	E385G	probably benign	Het
Psma6	A	T	12: 55,454,829 (GRCm39)	I53L	probably benign	Het
Ric8b	T	G	10: 84,783,761 (GRCm39)	D206E	probably benign	Het
Sardh	T	C	2: 27,079,559 (GRCm39)	D911G	probably benign	Het
Serpinb8	A	G	1: 107,534,776 (GRCm39)	T32A	unknown	Het
Shroom2	G	T	X: 151,443,035 (GRCm39)	T710K	probably benign	Het
Shroom3	G	T	5: 93,090,945 (GRCm39)	V1151F	probably damaging	Het
Slc38a7	A	G	8: 96,572,424 (GRCm39)		probably benign	Het
Stk36	T	A	1: 74,671,984 (GRCm39)	S895T	probably null	Het
Tbc1d16	A	T	11: 119,048,654 (GRCm39)	I333N	probably damaging	Het
Tectb	C	G	19: 55,169,431 (GRCm39)		probably benign	Het
Tmeff1	T	A	4: 48,658,831 (GRCm39)	Y101*	probably null	Het
Tns2	C	T	15: 102,017,369 (GRCm39)	R281C	probably damaging	Het
Ttn	T	A	2: 76,549,500 (GRCm39)	T23399S	probably damaging	Het
Vipas39	A	G	12: 87,289,297 (GRCm39)	V389A	possibly damaging	Het
Vps41	T	C	13: 18,994,598 (GRCm39)		probably benign	Het
Zfp329	A	T	7: 12,544,413 (GRCm39)	H370Q	probably damaging	Het
Zfp37	C	T	4: 62,110,014 (GRCm39)	G350D	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
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
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'- TGCTCAGATGTCTTAAGAAACTTAC -3'
(R):5'- GCTGCTGTTTCATGAAAGGAG -3'

Sequencing Primer
(F):5'- ATTGCCCAGACTAGCCTCAAATTTG -3'
(R):5'- CTGCTGTTTCATGAAAGGAGATATG -3'

Posted On

2015-01-23