Mutagenetix > Incidental Mutation

Incidental Mutation 'R5393:Sycp1'

425946

Institutional Source

Beutler Lab

Gene Symbol

Sycp1

Ensembl Gene

ENSMUSG00000027855

Gene Name

synaptonemal complex protein 1

Synonyms

SCP1

MMRRC Submission

042965-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.601) question?

Stock #

R5393 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

102818499-102936100 bp(-) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

T to C at 102841047 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000143651 (fasta)

Gene Model

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

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855

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

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.9%

Validation Efficiency

99% (72/73)

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110025L11Rik	A	T	16: 89,063,765	Y60*	probably null	Het
2810403A07Rik	T	A	3: 88,696,606	H243Q	probably benign	Het
Abca6	T	A	11: 110,244,295	E221D	probably benign	Het
Acyp2	C	T	11: 30,506,354	E98K	possibly damaging	Het
Adi1	A	G	12: 28,675,275	D8G	probably benign	Het
Adnp	T	C	2: 168,182,949	K809E	possibly damaging	Het
Aldh18a1	T	C	19: 40,585,567	H4R	probably benign	Het
Atp6v0a1	T	C	11: 101,038,807	S485P	possibly damaging	Het
C1galt1	T	C	6: 7,864,143		probably null	Het
Cacna2d4	A	T	6: 119,239,054	N94I	probably benign	Het
Catsperg1	T	C	7: 29,185,499	N899S	probably damaging	Het
Coro2a	A	G	4: 46,542,255	S373P	probably damaging	Het
Cpsf6	G	C	10: 117,362,016		probably benign	Het
Csmd3	A	T	15: 47,633,703	N3099K	probably damaging	Het
Ctla2b	T	A	13: 60,896,132	E74D	probably damaging	Het
Dnah2	T	A	11: 69,500,857	T671S	probably benign	Het
Drd5	T	A	5: 38,320,905	S414T	probably benign	Het
Dyrk2	C	T	10: 118,859,848	D502N	probably damaging	Het
Ecel1	A	T	1: 87,152,876	L376Q	possibly damaging	Het
Efcab8	G	A	2: 153,780,983	R24Q	unknown	Het
Eloc	A	C	1: 16,647,968		probably benign	Het
Ep300	A	G	15: 81,631,618		probably benign	Het
Fam89b	T	C	19: 5,728,705	D152G	probably damaging	Het
Gm15455	G	A	1: 33,836,846		noncoding transcript	Het
Greb1l	A	G	18: 10,458,312	T30A	probably benign	Het
Hdac10	T	C	15: 89,126,684	Y238C	probably damaging	Het
Ick	A	G	9: 78,160,715	T463A	probably benign	Het
Ighv2-5	T	C	12: 113,685,882	T12A	possibly damaging	Het
Insrr	T	C	3: 87,810,700		probably null	Het
Irf9	T	C	14: 55,606,457		probably benign	Het
Itpr2	A	T	6: 146,376,155	C280*	probably null	Het
Kcnk18	T	C	19: 59,219,839	C36R	probably damaging	Het
Klhl14	G	T	18: 21,651,994	N125K	probably benign	Het
Lce1i	T	C	3: 92,777,735	S45G	unknown	Het
Lrmda	A	C	14: 22,027,306	D37A	probably damaging	Het
Marco	A	C	1: 120,485,854	D280E	probably damaging	Het
Miox	C	T	15: 89,336,247	Q180*	probably null	Het
Npdc1	A	T	2: 25,408,670	M265L	probably damaging	Het
Nudcd3	T	C	11: 6,113,274	K205R	probably damaging	Het
Olfr319	T	A	11: 58,702,500	H266Q	probably damaging	Het
Olfr325	C	G	11: 58,580,999	L52V	possibly damaging	Het
Pcdhga5	C	T	18: 37,696,667	R723C	probably benign	Het
Pdlim5	T	A	3: 142,259,186	E295D	probably damaging	Het
Poli	C	A	18: 70,517,428	E314*	probably null	Het
Ptpro	A	G	6: 137,380,224	N238D	probably benign	Het
R3hdm1	A	G	1: 128,231,347	I920V	probably benign	Het
Ralgapa2	C	T	2: 146,345,455	V1338M	probably damaging	Het
Saa3	T	C	7: 46,712,661	Y53C	probably damaging	Het
Sept14	T	A	5: 129,683,586	E398D	probably benign	Het
Six3	T	C	17: 85,623,842	S309P	possibly damaging	Het
Slc7a14	A	G	3: 31,257,770	S34P	probably damaging	Het
Smarca2	C	A	19: 26,640,429	Q287K	probably benign	Het
Stard9	C	T	2: 120,702,906	L522F	possibly damaging	Het
Tbc1d8	A	T	1: 39,426,088	V73E	probably damaging	Het
Tldc1	T	C	8: 119,772,418	I112V	probably benign	Het
Tmem120a	T	C	5: 135,736,250		probably null	Het
Tsc2	T	C	17: 24,600,396	E1251G	possibly damaging	Het
Vps51	T	G	19: 6,071,033	E283D	probably benign	Het
Wnt5b	A	C	6: 119,440,433	L157R	probably damaging	Het
Zbtb24	T	A	10: 41,464,582	V536E	probably damaging	Het
Zfp593	G	A	4: 134,245,304	A67V	probably benign	Het
Zfp995	A	T	17: 21,880,492	F254I	probably benign	Het

Other mutations in Sycp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00513:Sycp1	APN	3	102840962	missense	probably benign
IGL00833:Sycp1	APN	3	102876301	critical splice donor site	probably null
IGL01066:Sycp1	APN	3	102920634	missense	probably damaging	1.00
IGL01484:Sycp1	APN	3	102915867	missense	probably benign	0.01
IGL02139:Sycp1	APN	3	102865114	missense	probably benign	0.00
IGL02270:Sycp1	APN	3	102895943	missense	probably benign	0.12
IGL02347:Sycp1	APN	3	102893547	missense	probably benign	0.00
IGL02630:Sycp1	APN	3	102878764	splice site	probably benign
IGL02668:Sycp1	APN	3	102820531	splice site	probably benign
IGL02928:Sycp1	APN	3	102818818	utr 3 prime	probably benign
PIT4458001:Sycp1	UTSW	3	102934833	missense	probably benign	0.01
R0027:Sycp1	UTSW	3	102895910	missense	probably benign
R0282:Sycp1	UTSW	3	102915795	splice site	probably benign
R0462:Sycp1	UTSW	3	102819106	missense	possibly damaging	0.75
R0609:Sycp1	UTSW	3	102898849	splice site	probably null
R0837:Sycp1	UTSW	3	102915245	missense	probably benign	0.17
R1301:Sycp1	UTSW	3	102920622	missense	probably benign	0.02
R2408:Sycp1	UTSW	3	102925259	missense	probably damaging	1.00
R2449:Sycp1	UTSW	3	102925206	missense	probably benign	0.15
R2516:Sycp1	UTSW	3	102845066	missense	probably benign	0.09
R2880:Sycp1	UTSW	3	102818898	missense	probably damaging	0.99
R3410:Sycp1	UTSW	3	102841041	missense	possibly damaging	0.94
R3427:Sycp1	UTSW	3	102876350	missense	probably benign	0.00
R4538:Sycp1	UTSW	3	102840962	missense	probably benign
R4679:Sycp1	UTSW	3	102922462	critical splice acceptor site	probably null
R4707:Sycp1	UTSW	3	102853489	missense	possibly damaging	0.92
R4785:Sycp1	UTSW	3	102853489	missense	possibly damaging	0.92
R5017:Sycp1	UTSW	3	102895987	splice site	probably null
R5036:Sycp1	UTSW	3	102820600	missense	probably damaging	1.00
R5044:Sycp1	UTSW	3	102845054	missense	probably benign	0.03
R5070:Sycp1	UTSW	3	102920565	missense	probably damaging	0.97
R5079:Sycp1	UTSW	3	102878800	missense	possibly damaging	0.67
R5289:Sycp1	UTSW	3	102934253	missense	possibly damaging	0.85
R5477:Sycp1	UTSW	3	102818890	missense	probably damaging	1.00
R5576:Sycp1	UTSW	3	102818902	missense	probably damaging	0.98
R5814:Sycp1	UTSW	3	102895897	missense	probably benign	0.03
R6291:Sycp1	UTSW	3	102908961	missense	probably damaging	1.00
R6460:Sycp1	UTSW	3	102925253	missense	probably damaging	1.00
R6527:Sycp1	UTSW	3	102898887	missense	probably benign	0.09
R6870:Sycp1	UTSW	3	102935603	missense	probably damaging	1.00
R6873:Sycp1	UTSW	3	102840980	missense	probably benign
R7037:Sycp1	UTSW	3	102898934	missense	possibly damaging	0.62
R7210:Sycp1	UTSW	3	102853492	missense	probably damaging	1.00
R7405:Sycp1	UTSW	3	102925227	missense	possibly damaging	0.72
R7604:Sycp1	UTSW	3	102913433	missense	probably damaging	0.98
R7733:Sycp1	UTSW	3	102895962	missense	probably benign	0.00
R7858:Sycp1	UTSW	3	102898957	missense	probably benign	0.09
R7909:Sycp1	UTSW	3	102820626	nonsense	probably null
R8109:Sycp1	UTSW	3	102851602	missense	probably benign	0.21
R8141:Sycp1	UTSW	3	102935569	missense	possibly damaging	0.73
R8289:Sycp1	UTSW	3	102841037	missense	probably benign	0.01
R8359:Sycp1	UTSW	3	102820593	missense	probably damaging	0.98
R8844:Sycp1	UTSW	3	102865105	missense	probably damaging	1.00
R9020:Sycp1	UTSW	3	102876337	missense	probably benign	0.01
R9149:Sycp1	UTSW	3	102851628	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTTCATGCTGAAAGGTCTTTGC -3'
(R):5'- TTTCTCACAATTGGAGCAGATGCC -3'

Sequencing Primer
(F):5'- CTTTGTAACTGTTGTAGGTAAAATGC -3'
(R):5'- GAGCAGATGCCCATTTTTCAG -3'

Posted On

2016-08-04