Mutagenetix > Incidental Mutation

Incidental Mutation 'R0609:Sycp1'

54496

Institutional Source

Beutler Lab

Gene Symbol

Sycp1

Ensembl Gene

ENSMUSG00000027855

Gene Name

synaptonemal complex protein 1

Synonyms

SCP1

MMRRC Submission

038798-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.539) question?

Stock #

R0609 (G1)

Quality Score

125

Status

Not validated

Chromosome

Chromosomal Location

102725815-102843416 bp(-) (GRCm39)

Type of Mutation

splice site (5 bp from exon)

DNA Base Change (assembly)

C to A at 102806165 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000143651 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029448] [ENSMUST00000029448] [ENSMUST00000029448] [ENSMUST00000196988] [ENSMUST00000196988] [ENSMUST00000196988]

AlphaFold

Q62209

Predicted Effect

probably null
Transcript: ENSMUST00000029448

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	809	N/A	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000029448

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	809	N/A	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000029448

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	809	N/A	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000196988

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	809	N/A	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000196988

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	809	N/A	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000196988

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	809	N/A	PFAM

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.6%
20x: 95.6%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Homozygous null mice display male and female infertility, azoospermia, small ovary, small testis and seminiferous tubules, absent ovarian follicles, and failure of synapse formation during meiosis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 103 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930596D02Rik	A	T	14: 35,533,418 (GRCm39)		probably null	Het
Abcb4	T	A	5: 8,997,376 (GRCm39)	C952S	probably damaging	Het
Adamtsl2	A	G	2: 26,979,647 (GRCm39)	D272G	probably benign	Het
Aim2	G	A	1: 173,289,530 (GRCm39)	D158N	probably damaging	Het
Aldh3b1	C	T	19: 3,964,024 (GRCm39)	R426H	probably damaging	Het
Apoc2	A	G	7: 19,407,278 (GRCm39)	S28P	probably benign	Het
Arfgef3	G	A	10: 18,473,179 (GRCm39)	T1628I	probably benign	Het
Atp10a	G	A	7: 58,469,488 (GRCm39)		probably null	Het
Bcl2	G	A	1: 106,640,292 (GRCm39)	R107C	probably damaging	Het
Bmp8b	T	A	4: 123,015,692 (GRCm39)	D226E	probably benign	Het
Brsk2	T	C	7: 141,552,229 (GRCm39)	Y618H	probably damaging	Het
Casp12	T	A	9: 5,346,554 (GRCm39)	F27Y	probably damaging	Het
Casp8	T	A	1: 58,883,951 (GRCm39)	N439K	probably benign	Het
Ccdc175	T	A	12: 72,204,281 (GRCm39)	K253N	probably benign	Het
Cdc42bpa	A	G	1: 179,867,744 (GRCm39)	H193R	probably damaging	Het
Cdk17	T	C	10: 93,052,334 (GRCm39)	M105T	probably benign	Het
Cdon	C	A	9: 35,389,907 (GRCm39)	P854T	probably damaging	Het
Cep44	A	G	8: 56,997,187 (GRCm39)	M117T	possibly damaging	Het
Cep89	A	T	7: 35,134,955 (GRCm39)	E674D	probably damaging	Het
Cit	C	T	5: 116,012,002 (GRCm39)	A203V	probably damaging	Het
Clstn1	C	A	4: 149,713,757 (GRCm39)		probably null	Het
Col7a1	T	A	9: 108,787,215 (GRCm39)	D565E	unknown	Het
Cpb1	T	A	3: 20,316,638 (GRCm39)	Y304F	probably damaging	Het
Cps1	T	G	1: 67,211,961 (GRCm39)	Y710D	probably damaging	Het
Creb3l1	T	C	2: 91,817,398 (GRCm39)	T372A	possibly damaging	Het
Dars1	A	G	1: 128,333,118 (GRCm39)	V102A	probably benign	Het
Dhx35	C	T	2: 158,659,335 (GRCm39)	T168I	possibly damaging	Het
Dnah5	T	C	15: 28,327,925 (GRCm39)	S2100P	probably benign	Het
Dst	T	C	1: 34,306,041 (GRCm39)		probably null	Het
Egflam	A	C	15: 7,283,004 (GRCm39)	L351R	possibly damaging	Het
Elp2	T	A	18: 24,759,213 (GRCm39)	D523E	probably benign	Het
Exo5	C	A	4: 120,778,881 (GRCm39)	G328V	probably damaging	Het
Fut9	A	G	4: 25,620,811 (GRCm39)	M1T	probably null	Het
Galnt5	A	G	2: 57,914,637 (GRCm39)	N584S	possibly damaging	Het
Gbp3	T	C	3: 142,273,533 (GRCm39)	V360A	probably damaging	Het
Gdf6	G	A	4: 9,859,977 (GRCm39)	C353Y	probably damaging	Het
Hace1	A	G	10: 45,524,965 (GRCm39)	T244A	probably damaging	Het
Hr	T	C	14: 70,797,097 (GRCm39)	I500T	probably benign	Het
Ifnl2	A	T	7: 28,208,707 (GRCm39)	L115Q	probably damaging	Het
Iigp1	T	C	18: 60,522,896 (GRCm39)	F5L	probably benign	Het
Inhbb	A	G	1: 119,345,146 (GRCm39)	L381P	probably damaging	Het
Irx3	A	T	8: 92,527,721 (GRCm39)	S50T	probably benign	Het
Ivns1abp	C	T	1: 151,235,896 (GRCm39)	T363I	probably benign	Het
Izumo1	A	T	7: 45,272,323 (GRCm39)	T35S	probably benign	Het
Kank4	A	G	4: 98,665,342 (GRCm39)	S651P	probably damaging	Het
Kit	T	C	5: 75,771,539 (GRCm39)	V232A	probably benign	Het
Klhl11	T	C	11: 100,354,540 (GRCm39)	Y427C	probably damaging	Het
Laptm4b	T	A	15: 34,258,835 (GRCm39)	N36K	probably damaging	Het
Lrrk1	T	C	7: 65,916,363 (GRCm39)		probably null	Het
Mamdc4	G	T	2: 25,454,205 (GRCm39)	Q1042K	probably benign	Het
Mical2	A	G	7: 111,920,647 (GRCm39)		probably null	Het
Ms4a3	C	A	19: 11,608,725 (GRCm39)	V176F	possibly damaging	Het
Myo3a	T	C	2: 22,338,324 (GRCm39)	V427A	probably benign	Het
Myo3a	A	C	2: 22,401,110 (GRCm39)	E626D	possibly damaging	Het
Nckap5	A	T	1: 125,955,025 (GRCm39)	L509*	probably null	Het
Ndufa5	A	T	6: 24,519,248 (GRCm39)	D64E	possibly damaging	Het
Nedd4l	T	C	18: 65,341,532 (GRCm39)	Y753H	probably damaging	Het
Nynrin	T	C	14: 56,110,218 (GRCm39)	V1775A	probably damaging	Het
Oplah	A	G	15: 76,187,192 (GRCm39)	S570P	probably benign	Het
Or14c39	T	C	7: 86,344,084 (GRCm39)	V140A	possibly damaging	Het
Or2ag1b	A	T	7: 106,288,205 (GRCm39)	H244Q	probably damaging	Het
Or4q3	T	C	14: 50,583,383 (GRCm39)	Y141C	probably damaging	Het
Or5t18	A	G	2: 86,637,205 (GRCm39)	L46S	probably damaging	Het
Or9r3	G	A	10: 129,948,449 (GRCm39)	S70F	probably damaging	Het
Osbpl11	C	A	16: 33,054,814 (GRCm39)	Y632*	probably null	Het
Osbpl5	A	T	7: 143,248,558 (GRCm39)	L644Q	probably damaging	Het
Pcdhb19	T	C	18: 37,631,005 (GRCm39)	W267R	probably benign	Het
Pkhd1l1	A	C	15: 44,330,820 (GRCm39)	S132R	possibly damaging	Het
Pramel23	A	T	4: 143,425,073 (GRCm39)	D123E	probably benign	Het
Ptpn13	T	A	5: 103,704,011 (GRCm39)	S1348T	probably benign	Het
Rc3h1	T	A	1: 160,757,705 (GRCm39)	W8R	probably damaging	Het
Rgs3	T	G	4: 62,544,173 (GRCm39)	V315G	probably damaging	Het
Rora	T	A	9: 69,269,151 (GRCm39)	M82K	probably damaging	Het
Rph3al	T	C	11: 75,799,795 (GRCm39)	I55V	probably benign	Het
Sag	T	C	1: 87,740,713 (GRCm39)	V45A	probably damaging	Het
Scn3a	T	C	2: 65,366,854 (GRCm39)	E56G	probably damaging	Het
Sec24c	T	G	14: 20,737,016 (GRCm39)	V324G	probably damaging	Het
Sptbn1	A	G	11: 30,088,979 (GRCm39)	L748S	probably damaging	Het
Stard9	A	T	2: 120,536,787 (GRCm39)	D4186V	probably damaging	Het
Stk39	T	C	2: 68,196,511 (GRCm39)	E306G	probably damaging	Het
Taf2	A	C	15: 54,923,446 (GRCm39)	L277R	probably damaging	Het
Tasor	C	T	14: 27,183,707 (GRCm39)	T722I	probably benign	Het
Tbc1d23	T	A	16: 56,993,469 (GRCm39)	I566F	possibly damaging	Het
Tekt5	T	C	16: 10,179,168 (GRCm39)	T400A	possibly damaging	Het
Tgfbrap1	T	C	1: 43,099,301 (GRCm39)	H401R	probably benign	Het
Tie1	T	A	4: 118,333,344 (GRCm39)	I841L	possibly damaging	Het
Tln1	T	G	4: 43,544,645 (GRCm39)	T1095P	possibly damaging	Het
Tmem147	A	G	7: 30,427,527 (GRCm39)	Y72H	probably benign	Het
Tnfaip2	A	G	12: 111,419,941 (GRCm39)	N691S	probably benign	Het
Trim24	G	A	6: 37,934,718 (GRCm39)	C811Y	probably damaging	Het
Trim30b	T	A	7: 104,007,183 (GRCm39)		probably benign	Het
Trpc4	T	G	3: 54,102,189 (GRCm39)	L29R	probably damaging	Het
Trpm6	A	T	19: 18,803,226 (GRCm39)	I890F	probably damaging	Het
Ttc23l	C	T	15: 10,504,622 (GRCm39)	E442K	probably benign	Het
Tut7	A	T	13: 59,947,596 (GRCm39)	C506*	probably null	Het
Uggt2	A	G	14: 119,332,748 (GRCm39)	V62A	probably damaging	Het
Ugt1a6a	C	A	1: 88,066,606 (GRCm39)	S137R	probably benign	Het
Unc13a	A	G	8: 72,111,111 (GRCm39)	Y367H	probably damaging	Het
Vmn2r49	A	G	7: 9,710,233 (GRCm39)	I833T	probably benign	Het
Vmn2r7	T	C	3: 64,623,900 (GRCm39)	D231G	probably benign	Het
Ythdc2	A	T	18: 44,997,424 (GRCm39)	M994L	probably benign	Het
Zfp804a	G	A	2: 82,087,932 (GRCm39)	S587N	probably damaging	Het
Zswim2	A	G	2: 83,754,003 (GRCm39)	I219T	probably benign	Het

Other mutations in Sycp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00513:Sycp1	APN	3	102,748,278 (GRCm39)	missense	probably benign
IGL00833:Sycp1	APN	3	102,783,617 (GRCm39)	critical splice donor site	probably null
IGL01066:Sycp1	APN	3	102,827,950 (GRCm39)	missense	probably damaging	1.00
IGL01484:Sycp1	APN	3	102,823,183 (GRCm39)	missense	probably benign	0.01
IGL02139:Sycp1	APN	3	102,772,430 (GRCm39)	missense	probably benign	0.00
IGL02270:Sycp1	APN	3	102,803,259 (GRCm39)	missense	probably benign	0.12
IGL02347:Sycp1	APN	3	102,800,863 (GRCm39)	missense	probably benign	0.00
IGL02630:Sycp1	APN	3	102,786,080 (GRCm39)	splice site	probably benign
IGL02668:Sycp1	APN	3	102,727,847 (GRCm39)	splice site	probably benign
IGL02928:Sycp1	APN	3	102,726,134 (GRCm39)	utr 3 prime	probably benign
PIT4458001:Sycp1	UTSW	3	102,842,149 (GRCm39)	missense	probably benign	0.01
R0027:Sycp1	UTSW	3	102,803,226 (GRCm39)	missense	probably benign
R0282:Sycp1	UTSW	3	102,823,111 (GRCm39)	splice site	probably benign
R0462:Sycp1	UTSW	3	102,726,422 (GRCm39)	missense	possibly damaging	0.75
R0837:Sycp1	UTSW	3	102,822,561 (GRCm39)	missense	probably benign	0.17
R1301:Sycp1	UTSW	3	102,827,938 (GRCm39)	missense	probably benign	0.02
R2408:Sycp1	UTSW	3	102,832,575 (GRCm39)	missense	probably damaging	1.00
R2449:Sycp1	UTSW	3	102,832,522 (GRCm39)	missense	probably benign	0.15
R2516:Sycp1	UTSW	3	102,752,382 (GRCm39)	missense	probably benign	0.09
R2880:Sycp1	UTSW	3	102,726,214 (GRCm39)	missense	probably damaging	0.99
R3410:Sycp1	UTSW	3	102,748,357 (GRCm39)	missense	possibly damaging	0.94
R3427:Sycp1	UTSW	3	102,783,666 (GRCm39)	missense	probably benign	0.00
R4538:Sycp1	UTSW	3	102,748,278 (GRCm39)	missense	probably benign
R4679:Sycp1	UTSW	3	102,829,778 (GRCm39)	critical splice acceptor site	probably null
R4707:Sycp1	UTSW	3	102,760,805 (GRCm39)	missense	possibly damaging	0.92
R4785:Sycp1	UTSW	3	102,760,805 (GRCm39)	missense	possibly damaging	0.92
R5017:Sycp1	UTSW	3	102,803,303 (GRCm39)	splice site	probably null
R5036:Sycp1	UTSW	3	102,727,916 (GRCm39)	missense	probably damaging	1.00
R5044:Sycp1	UTSW	3	102,752,370 (GRCm39)	missense	probably benign	0.03
R5070:Sycp1	UTSW	3	102,827,881 (GRCm39)	missense	probably damaging	0.97
R5079:Sycp1	UTSW	3	102,786,116 (GRCm39)	missense	possibly damaging	0.67
R5289:Sycp1	UTSW	3	102,841,569 (GRCm39)	missense	possibly damaging	0.85
R5393:Sycp1	UTSW	3	102,748,363 (GRCm39)	splice site	probably null
R5477:Sycp1	UTSW	3	102,726,206 (GRCm39)	missense	probably damaging	1.00
R5576:Sycp1	UTSW	3	102,726,218 (GRCm39)	missense	probably damaging	0.98
R5814:Sycp1	UTSW	3	102,803,213 (GRCm39)	missense	probably benign	0.03
R6291:Sycp1	UTSW	3	102,816,277 (GRCm39)	missense	probably damaging	1.00
R6460:Sycp1	UTSW	3	102,832,569 (GRCm39)	missense	probably damaging	1.00
R6527:Sycp1	UTSW	3	102,806,203 (GRCm39)	missense	probably benign	0.09
R6870:Sycp1	UTSW	3	102,842,919 (GRCm39)	missense	probably damaging	1.00
R6873:Sycp1	UTSW	3	102,748,296 (GRCm39)	missense	probably benign
R7037:Sycp1	UTSW	3	102,806,250 (GRCm39)	missense	possibly damaging	0.62
R7210:Sycp1	UTSW	3	102,760,808 (GRCm39)	missense	probably damaging	1.00
R7405:Sycp1	UTSW	3	102,832,543 (GRCm39)	missense	possibly damaging	0.72
R7604:Sycp1	UTSW	3	102,820,749 (GRCm39)	missense	probably damaging	0.98
R7733:Sycp1	UTSW	3	102,803,278 (GRCm39)	missense	probably benign	0.00
R7858:Sycp1	UTSW	3	102,806,273 (GRCm39)	missense	probably benign	0.09
R7909:Sycp1	UTSW	3	102,727,942 (GRCm39)	nonsense	probably null
R8109:Sycp1	UTSW	3	102,758,918 (GRCm39)	missense	probably benign	0.21
R8141:Sycp1	UTSW	3	102,842,885 (GRCm39)	missense	possibly damaging	0.73
R8289:Sycp1	UTSW	3	102,748,353 (GRCm39)	missense	probably benign	0.01
R8359:Sycp1	UTSW	3	102,727,909 (GRCm39)	missense	probably damaging	0.98
R8844:Sycp1	UTSW	3	102,772,421 (GRCm39)	missense	probably damaging	1.00
R9020:Sycp1	UTSW	3	102,783,653 (GRCm39)	missense	probably benign	0.01
R9149:Sycp1	UTSW	3	102,758,944 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCTTTTGACTACAAAGCACGGTcc -3'
(R):5'- caccatgcccagcCTAACTATGTC -3'

Sequencing Primer
(F):5'- gtaatcctcttgcttcagcttc -3'
(R):5'- GCAAGAACAAGTAACTGTCACTA -3'

Posted On

2013-07-11