Mutagenetix > Incidental Mutation

Incidental Mutation 'R7733:Sycp1'

595969

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 non essential (E-score: 0.477) question?

Stock #

R7733 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

102818499-102936100 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 102895962 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 511 (T511A)

Ref Sequence

ENSEMBL: ENSMUSP00000029448 (fasta)

Gene Model

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

AlphaFold

Q62209

Predicted Effect

probably benign
Transcript: ENSMUST00000029448
AA Change: T511A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: T511A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000196988
AA Change: T511A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: T511A

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.3%

Validation Efficiency

100% (83/83)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5530400C23Rik	T	A	6: 133,294,277	S95T	probably benign	Het
9530053A07Rik	A	T	7: 28,139,965	D401V	probably damaging	Het
Abca8a	A	G	11: 110,054,587	F1070L	probably benign	Het
Acsl3	G	C	1: 78,688,236		probably null	Het
Adarb2	T	A	13: 8,752,608	S640T	possibly damaging	Het
Adgre5	T	C	8: 83,729,396	D257G	probably benign	Het
Adora2b	A	T	11: 62,265,339	I205F	possibly damaging	Het
Asb14	A	G	14: 26,912,352	M505V	probably benign	Het
Atrnl1	T	C	19: 57,701,988	V876A	probably benign	Het
AU040320	A	G	4: 126,835,529	N495D	possibly damaging	Het
BC005561	T	C	5: 104,519,960	F783L	possibly damaging	Het
Bcam	A	T	7: 19,760,388	V361E	probably benign	Het
Cbwd1	T	C	19: 24,940,794	D204G	probably damaging	Het
Ccdc7a	T	A	8: 128,993,052	E247V	probably damaging	Het
Cd84	T	A	1: 171,840,659	M1K	probably null	Het
Cfap43	C	T	19: 47,897,993	R61H	possibly damaging	Het
Clec4a1	A	G	6: 122,932,150	D159G	possibly damaging	Het
Ctcfl	C	T	2: 173,117,192	R247Q	probably benign	Het
Ctdnep1	G	A	11: 69,990,009	R236Q	probably damaging	Het
Cwf19l2	A	T	9: 3,450,066	H589L	probably benign	Het
Cyp2u1	G	T	3: 131,303,027	A34E	probably benign	Het
Cyp4x1	A	G	4: 115,120,194	S281P	possibly damaging	Het
Dag1	T	C	9: 108,208,848	T365A	probably benign	Het
Dhx57	A	T	17: 80,265,074		probably null	Het
Dnajb1	T	G	8: 83,608,377	S16A	probably benign	Het
Dsc2	A	T	18: 20,048,315	L145Q	probably benign	Het
Dsc2	G	C	18: 20,048,316	L145V	probably benign	Het
Eefsec	T	C	6: 88,376,220	T156A	possibly damaging	Het
Eif6	T	A	2: 155,823,232	D169V	probably benign	Het
Ell3	C	A	2: 121,442,520	G3V	possibly damaging	Het
Eprs	A	T	1: 185,397,161	H615L	probably benign	Het
Fbxw10	A	G	11: 62,873,397	Y630C	unknown	Het
G6pc2	C	T	2: 69,220,183	Q51*	probably null	Het
Glt8d1	C	T	14: 31,001,978		probably benign	Het
Gm16486	A	G	8: 70,717,451	T1397A	possibly damaging	Het
Gpr4	T	C	7: 19,222,710	Y186H	probably damaging	Het
Grhpr	T	C	4: 44,981,494		probably benign	Het
Gsdma3	A	G	11: 98,635,215	H264R	probably damaging	Het
Hcfc2	A	G	10: 82,739,179	Y224C	probably benign	Het
Helz2	A	G	2: 181,230,355	F2608S	possibly damaging	Het
Herc2	C	T	7: 56,188,664	T3313M	probably damaging	Het
Hmgcl	A	T	4: 135,960,083	H223L	probably benign	Het
Igf2r	A	G	17: 12,739,369	V139A	possibly damaging	Het
Kif5a	T	A	10: 127,236,740	T727S	probably benign	Het
Kifc1	G	A	17: 33,883,569	R357W	probably damaging	Het
Krt81	T	A	15: 101,463,514	S62C	probably damaging	Het
Lgi2	T	C	5: 52,538,531	N362S	probably benign	Het
Lig1	G	T	7: 13,296,231	R378L	possibly damaging	Het
Map3k13	C	T	16: 21,921,686	R588C	probably damaging	Het
Mov10l1	T	A	15: 89,024,801	F1008L	probably damaging	Het
Nr4a2	A	G	2: 57,112,321	V40A	probably benign	Het
Nrde2	A	T	12: 100,144,140	C206S	possibly damaging	Het
Olfr1316	C	T	2: 112,130,041	V257I	probably benign	Het
Parp1	T	C	1: 180,600,212		probably null	Het
Pcdhb12	A	G	18: 37,437,036	T412A	probably damaging	Het
Plekhh2	T	A	17: 84,583,524	Y839*	probably null	Het
Pnpla6	T	A	8: 3,522,660	F316I	probably benign	Het
Prcp	C	T	7: 92,901,298	T101M	probably damaging	Het
Prex2	G	T	1: 11,181,959	R1076L	probably benign	Het
Prpf40b	T	C	15: 99,308,343		probably null	Het
Psd3	T	G	8: 68,120,916	K204N	possibly damaging	Het
Ptpro	C	A	6: 137,414,286	C801*	probably null	Het
Ptprt	A	G	2: 161,575,787	V923A	probably damaging	Het
Ptprz1	T	A	6: 23,000,384	D824E	probably benign	Het
Rasgrf1	A	G	9: 89,981,727	D582G	probably benign	Het
Rfc2	T	C	5: 134,593,216	L183P	probably damaging	Het
Rnf114	T	C	2: 167,512,518	V173A	probably damaging	Het
Scn3a	T	A	2: 65,508,650	I562F	probably benign	Het
Setmar	T	C	6: 108,076,127	I194T	probably damaging	Het
Sptb	A	T	12: 76,597,921		probably null	Het
Sptbn2	C	G	19: 4,749,012	R2037G	probably benign	Het
Sptlc3	G	T	2: 139,631,368	M512I	possibly damaging	Het
Svep1	C	A	4: 58,049,239	A3423S	probably benign	Het
Synm	T	A	7: 67,735,945		probably null	Het
Tada1	C	T	1: 166,389,942	P216L	probably damaging	Het
Tas2r117	T	A	6: 132,803,175	M92K	probably benign	Het
Thsd1	T	C	8: 22,258,721	L536P	probably damaging	Het
Timp2	T	G	11: 118,317,529		probably null	Het
Trak1	T	A	9: 121,367,225	V41D	possibly damaging	Het
Ubqln3	T	A	7: 104,141,076	L602F	probably damaging	Het
Vmn2r59	A	G	7: 42,012,019	F791L	probably benign	Het
Wbp4	A	G	14: 79,477,040		probably null	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
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
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'- TGTGCAGGAATAGAAACCCTG -3'
(R):5'- ACGACTTTGTAAGAATGGTTGC -3'

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

Posted On

2019-11-12