Mutagenetix > Incidental Mutation

Incidental Mutation 'R6527:Sycp1'

521942

Institutional Source

Beutler Lab

Gene Symbol

Sycp1

Ensembl Gene

ENSMUSG00000027855

Gene Name

synaptonemal complex protein 1

Synonyms

SCP1

MMRRC Submission

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.601) question?

Stock #

R6527 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

102818499-102936100 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 102898887 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 496 (V496A)

Ref Sequence

ENSEMBL: ENSMUSP00000143651 (fasta)

Gene Model

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

AlphaFold

Q62209

Predicted Effect

probably benign
Transcript: ENSMUST00000029448
AA Change: V496A

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: V496A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000196988
AA Change: V496A

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: V496A

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

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.9%
20x: 93.7%

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: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	G	3: 138,067,527	T826A	probably damaging	Het
Abca16	T	A	7: 120,477,772	I686N	possibly damaging	Het
Abcb6	T	C	1: 75,177,488		probably null	Het
Adgrl3	A	C	5: 81,787,517	E1299A	probably damaging	Het
Als2cr12	T	C	1: 58,692,413	M1V	probably null	Het
Amd2	A	C	10: 35,710,806	Y252D	probably damaging	Het
Cfap74	A	G	4: 155,422,265		probably null	Het
Dhx29	G	T	13: 112,932,542	K135N	probably damaging	Het
Dlg5	T	A	14: 24,190,448	D245V	possibly damaging	Het
Dscaml1	C	T	9: 45,712,184	Q83*	probably null	Het
Dsp	T	A	13: 38,195,873	L1599Q	probably damaging	Het
Duox2	A	G	2: 122,294,614	V369A	probably benign	Het
Gbe1	T	A	16: 70,433,672		probably null	Het
Gm7298	A	G	6: 121,769,710	K600R	probably benign	Het
Heatr4	C	T	12: 83,979,763	G240E	probably damaging	Het
Jakmip2	A	G	18: 43,556,524	V651A	possibly damaging	Het
Jam3	C	T	9: 27,155,344	R8Q	unknown	Het
Letm2	A	G	8: 25,592,506		probably benign	Het
Lmod3	T	C	6: 97,247,378	D494G	probably benign	Het
Mast2	T	C	4: 116,314,939	D604G	probably damaging	Het
Mif4gd	C	T	11: 115,609,275		probably null	Het
Msr1	T	C	8: 39,624,233	E112G	possibly damaging	Het
Mtus2	A	G	5: 148,277,598		probably null	Het
Muc4	A	G	16: 32,753,433	H1103R	probably benign	Het
Nudt14	T	A	12: 112,934,887	I198F	possibly damaging	Het
Olfr1341	T	A	4: 118,709,848	F147Y	possibly damaging	Het
Olfr353	T	C	2: 36,890,582	T89A	probably benign	Het
Olfr736	T	A	14: 50,393,428	L224*	probably null	Het
Osbpl8	T	C	10: 111,293,205	I884T	probably benign	Het
Podxl2	T	C	6: 88,842,930	N550S	probably damaging	Het
Ppp1r9a	A	G	6: 5,045,949	Y151C	probably damaging	Het
Prss42	T	C	9: 110,800,856	V226A	possibly damaging	Het
Psmd12	A	G	11: 107,488,968	I116V	probably damaging	Het
Psme4	A	C	11: 30,832,175	I872L	probably benign	Het
Rab11fip1	A	T	8: 27,174,392	V65E	probably damaging	Het
Ros1	T	C	10: 52,143,377	N700S	possibly damaging	Het
Slc15a4	G	A	5: 127,596,709	T547M	probably damaging	Het
Slfn3	T	A	11: 83,213,106	C268S	probably benign	Het
Smc5	T	C	19: 23,228,190	Q794R	probably benign	Het
Sqor	A	G	2: 122,809,286	Y434C	probably damaging	Het
Steap4	T	A	5: 7,978,502	L360H	probably damaging	Het
Tmem161b	T	G	13: 84,272,264	M128R	probably benign	Het
Tmem59l	T	C	8: 70,486,125	E102G	probably damaging	Het
Tnks	A	T	8: 34,873,093	V457D	probably benign	Het
Tomt	A	G	7: 101,900,392	Y230H	probably damaging	Het
Trim37	A	G	11: 87,190,084	N561D	probably damaging	Het
V1ra8	T	A	6: 90,203,313	I166K	probably damaging	Het
Vmn1r56	A	G	7: 5,196,576	V14A	probably benign	Het
Vsig8	T	C	1: 172,560,358	V5A	possibly damaging	Het
Vwa8	A	T	14: 78,947,213	S384C	possibly damaging	Het
Wwc1	C	T	11: 35,853,437	E853K	probably benign	Het
Zfp984	T	C	4: 147,755,924	N157D	probably benign	Het
Zzef1	G	A	11: 72,874,990	D1448N	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
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
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'- AGCTTTTGACTACAAAGCACG -3'
(R):5'- GCCAAATTTTCTCCAATGTATTGCTTG -3'

Sequencing Primer
(F):5'- GCTTCAGCTTCCAGAGTACTGAG -3'
(R):5'- GAGACTGTCTATGGAACTCCTGC -3'

Posted On

2018-06-06