Mutagenetix > Incidental Mutation

Incidental Mutation 'R5017:Sycp1'

385606

Institutional Source

Beutler Lab

Gene Symbol

Sycp1

Ensembl Gene

ENSMUSG00000027855

Gene Name

synaptonemal complex protein 1

Synonyms

SCP1

MMRRC Submission

042608-MU

Accession Numbers

Is this an essential gene?

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

Stock #

R5017 (G1)

Quality Score

162

Status

Validated

Chromosome

Chromosomal Location

102818499-102936100 bp(-) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

A to T at 102895987 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000143651 (fasta)

Gene Model

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

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 98.1%
3x: 97.0%
10x: 94.3%
20x: 87.9%

Validation Efficiency

96% (46/48)

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932415D10Rik	A	T	10: 82,296,676	F167I	unknown	Het
Adamdec1	T	C	14: 68,573,245	D154G	probably benign	Het
Agbl5	G	A	5: 30,903,059	R141Q	probably damaging	Het
Arhgef3	G	T	14: 27,265,530	R20L	possibly damaging	Het
Birc2	A	T	9: 7,818,885	C568*	probably null	Het
Cep44	A	G	8: 56,544,207	S99P	possibly damaging	Het
Clstn2	A	G	9: 97,483,086	W456R	probably damaging	Het
Cog5	T	A	12: 31,920,605	S783T	probably benign	Het
Endod1	G	A	9: 14,356,891	R433*	probably null	Het
Fchsd1	C	T	18: 37,959,873		probably benign	Het
Gdpd4	C	A	7: 98,004,275	Y498*	probably null	Het
Gm10722	T	C	9: 3,000,937	C6R	probably benign	Het
Hapln2	A	G	3: 88,024,001	V69A	probably damaging	Het
Ifit3	A	C	19: 34,587,192	N46T	possibly damaging	Het
Kcnh8	T	C	17: 52,893,930	L464S	probably damaging	Het
Lrrc9	C	A	12: 72,506,325	R1334S	possibly damaging	Het
Macf1	A	G	4: 123,452,113	F2631L	probably damaging	Het
Mafa	T	C	15: 75,747,489	H145R	probably benign	Het
Muc6	T	C	7: 141,640,528	T1411A	probably benign	Het
Nos3	A	G	5: 24,366,719		probably benign	Het
Nwd2	T	A	5: 63,650,141		probably benign	Het
Olfr160	A	T	9: 37,711,525	Y251*	probably null	Het
Olfr44	A	T	9: 39,484,755	M166K	possibly damaging	Het
Olfr981	A	T	9: 40,022,376		probably benign	Het
Pde11a	A	T	2: 76,136,367	D579E	probably benign	Het
Phkb	A	T	8: 86,049,809	H954L	probably benign	Het
Phldb3	C	T	7: 24,620,096	T353M	probably damaging	Het
Pigu	A	T	2: 155,299,208		probably null	Het
Pla2r1	A	G	2: 60,522,760		probably null	Het
Polr1c	G	T	17: 46,247,709		probably benign	Het
Setbp1	C	A	18: 78,856,594	G1286V	possibly damaging	Het
Siglecg	T	A	7: 43,411,386		probably benign	Het
Slc25a46	A	T	18: 31,605,783	H118Q	probably damaging	Het
Tmem132c	A	G	5: 127,563,350	T862A	probably benign	Het
Tmem256	T	C	11: 69,838,992		probably benign	Het
Tpr	A	T	1: 150,398,637	E98D	probably benign	Het
Trdn	A	G	10: 33,468,159	D623G	probably benign	Het
Trip11	T	C	12: 101,846,620	N1485S	probably benign	Het
Trpm1	T	C	7: 64,244,832		probably benign	Het
Uhrf1bp1	T	A	17: 27,894,739	L1295*	probably null	Het
Vmn1r227	T	C	17: 20,736,078		noncoding transcript	Het
Xpo6	G	A	7: 126,104,747	A21V	probably benign	Het
Zfp276	A	G	8: 123,264,977		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
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'- AGTCCCTCTACTTTTGAAGTTAAGA -3'
(R):5'- ACGACTTTGTAAGAATGGTTGC -3'

Sequencing Primer
(F):5'- GGGCCATATCACTTGCTT -3'
(R):5'- GAGCAATTATGTGGAAAATATGTGC -3'

Posted On

2016-05-10