Mutagenetix > Incidental Mutation

Incidental Mutation 'R3410:Sycp1'

258449

Institutional Source

Beutler Lab

Gene Symbol

Sycp1

Ensembl Gene

ENSMUSG00000027855

Gene Name

synaptonemal complex protein 1

Synonyms

SCP1

MMRRC Submission

040628-MU

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.477) question?

Stock #

R3410 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

102818499-102936100 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 102841041 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamic Acid at position 812 (K812E)

Ref Sequence

ENSEMBL: ENSMUSP00000143651 (fasta)

Gene Model

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

AlphaFold

Q62209

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029448
AA Change: K812E

PolyPhen 2 Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: K812E

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000196988
AA Change: K812E

PolyPhen 2 Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: K812E

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

Meta Mutation Damage Score

0.0646

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.4%

Validation Efficiency

100% (59/59)

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: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adad2	T	C	8: 119,615,969	V418A	probably benign	Het
Adamts16	T	C	13: 70,753,226	T911A	probably benign	Het
Adgra1	T	C	7: 139,847,703	F62S	possibly damaging	Het
Adgra3	A	G	5: 50,001,930	V326A	probably damaging	Het
Adgrg6	A	G	10: 14,440,370	F569S	probably benign	Het
Alcam	T	C	16: 52,309,898	T30A	probably null	Het
Arnt2	G	A	7: 84,275,447	R391W	probably damaging	Het
Ascc3	T	C	10: 50,700,100	V817A	probably damaging	Het
Atp13a4	G	T	16: 29,413,749	T923K	probably damaging	Het
Atp5o	C	T	16: 91,928,906	R64H	probably damaging	Het
Ccdc185	T	G	1: 182,748,748	Q125H	possibly damaging	Het
Ccdc88a	T	A	11: 29,486,006	C10S	probably damaging	Het
Cct2	T	C	10: 117,062,063	N73S	probably benign	Het
Clock	G	A	5: 76,229,554	Q633*	probably null	Het
Col6a2	T	C	10: 76,603,359	I826V	probably benign	Het
Cpsf1	G	T	15: 76,601,781	Y396*	probably null	Het
Dnah1	A	T	14: 31,269,817	M3076K	possibly damaging	Het
Dxo	A	G	17: 34,838,849	N177D	probably damaging	Het
Fbxw28	A	T	9: 109,338,404	V95E	possibly damaging	Het
Galnt6	T	C	15: 100,699,137	N383D	probably damaging	Het
Gpat2	G	A	2: 127,428,291	V75M	probably damaging	Het
Grik5	T	C	7: 25,062,972	D198G	probably benign	Het
Gsdmc4	A	G	15: 63,892,046	S401P	probably benign	Het
Gspt1	A	T	16: 11,229,245	D435E	probably damaging	Het
Hsf2	T	C	10: 57,505,282	S266P	probably damaging	Het
Jade2	T	C	11: 51,817,223	D721G	probably benign	Het
Klhl7	G	T	5: 24,138,321	V212L	probably damaging	Het
Klra17	T	A	6: 129,874,846	N21I	probably damaging	Het
L3mbtl3	T	C	10: 26,339,299	N196S	unknown	Het
Lama3	G	C	18: 12,413,858		probably null	Het
Mcm5	T	C	8: 75,121,644	M507T	possibly damaging	Het
Mycbp2	T	C	14: 103,135,117	R814G	probably damaging	Het
Nlrp4b	A	G	7: 10,715,529	E186G	probably damaging	Het
Nlrp4c	A	G	7: 6,092,570	K816E	possibly damaging	Het
Nod1	G	T	6: 54,944,917	R139S	probably benign	Het
Nudcd1	T	C	15: 44,420,811	M60V	probably benign	Het
Olfr1453	G	C	19: 13,028,047	A94G	probably benign	Het
Olfr487	G	A	7: 108,212,283	P82L	possibly damaging	Het
Olfr494	A	T	7: 108,368,344	I285F	possibly damaging	Het
Olfr945	G	T	9: 39,258,601	Q24K	possibly damaging	Het
Ovol2	A	G	2: 144,317,876	S82P	probably benign	Het
Ppl	T	C	16: 5,107,517	E86G	possibly damaging	Het
Ptch1	T	G	13: 63,524,959	E944A	probably benign	Het
Ripk4	T	C	16: 97,743,957	T497A	probably benign	Het
Scml4	A	G	10: 42,957,671	Y327C	probably damaging	Het
Serpina3n	A	G	12: 104,411,277	E263G	possibly damaging	Het
Six4	A	G	12: 73,112,883	F101S	probably damaging	Het
Sltm	T	G	9: 70,585,958	L728V	probably damaging	Het
Sptb	T	G	12: 76,610,815	K1311Q	possibly damaging	Het
Tenm4	T	C	7: 96,852,530	Y1314H	probably damaging	Het
Tmem67	A	T	4: 12,073,952	M288K	probably benign	Het
Toporsl	T	C	4: 52,610,970	S288P	probably benign	Het
Ttn	A	C	2: 76,942,405	N2415K	possibly damaging	Het
Vmn2r65	T	C	7: 84,946,688	I263V	probably benign	Het
Vmn2r89	A	T	14: 51,456,171	E326V	probably damaging	Het
Wdr81	A	G	11: 75,452,932	I503T	probably damaging	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
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
R5393:Sycp1	UTSW	3	102841047	splice site	probably null
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'- TCACAATTGGAGCAGATGCCC -3'

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

Posted On

2015-01-23