Mutagenetix > Incidental Mutation

Incidental Mutation 'R9149:Sycp1'

694871

Institutional Source

Beutler Lab

Gene Symbol

Sycp1

Ensembl Gene

ENSMUSG00000027855

Gene Name

synaptonemal complex protein 1

Synonyms

SCP1

MMRRC Submission

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.539) question?

Stock #

R9149 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

102725815-102843416 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 102758944 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Arginine at position 771 (L771R)

Ref Sequence

ENSEMBL: ENSMUSP00000029448 (fasta)

Gene Model

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

AlphaFold

Q62209

Predicted Effect

probably damaging
Transcript: ENSMUST00000029448
AA Change: L771R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: L771R

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000196988
AA Change: L771R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: L771R

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

100% (90/90)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930505A04Rik	C	T	11: 30,396,304 (GRCm39)	S103N	probably benign	Het
Ace	A	G	11: 105,863,299 (GRCm39)	D358G	possibly damaging	Het
Acvr2b	A	T	9: 119,257,116 (GRCm39)	H115L	probably damaging	Het
Adam15	G	A	3: 89,254,742 (GRCm39)	T106I	possibly damaging	Het
Adamts16	A	G	13: 70,883,948 (GRCm39)	C1076R	probably damaging	Het
Adcy5	A	G	16: 35,092,481 (GRCm39)	Y614C	probably damaging	Het
Adhfe1	A	T	1: 9,627,276 (GRCm39)	H225L	probably benign	Het
Aff3	A	G	1: 38,220,397 (GRCm39)	I1171T	probably damaging	Het
Agps	T	A	2: 75,697,182 (GRCm39)	M334K	probably damaging	Het
Akr1e1	A	G	13: 4,652,678 (GRCm39)		probably null	Het
Als2cl	G	A	9: 110,718,191 (GRCm39)	V311M	probably benign	Het
Amdhd1	A	T	10: 93,375,813 (GRCm39)	L7H	probably damaging	Het
Apba1	A	T	19: 23,870,782 (GRCm39)	I205F	probably damaging	Het
Arhgap26	A	T	18: 39,244,917 (GRCm39)	E187D	possibly damaging	Het
Ash1l	A	T	3: 88,914,530 (GRCm39)	H1720L	probably benign	Het
Atp9a	T	C	2: 168,575,988 (GRCm39)		probably benign	Het
Bcl7c	G	A	7: 127,307,695 (GRCm39)	A2V	probably damaging	Het
Catsperg1	G	C	7: 28,909,912 (GRCm39)	P72R	probably benign	Het
Ccdc103	G	A	11: 102,774,922 (GRCm39)	G174R	probably benign	Het
Ccdc171	A	T	4: 83,612,512 (GRCm39)	K976M	probably damaging	Het
Ceacam1	T	C	7: 25,173,360 (GRCm39)	N276S	possibly damaging	Het
Cep152	T	C	2: 125,463,127 (GRCm39)	E18G	probably damaging	Het
Cep152	T	C	2: 125,461,803 (GRCm39)	N91S	probably damaging	Het
Cers3	T	C	7: 66,393,442 (GRCm39)	L17P	probably benign	Het
Cpsf3	A	G	12: 21,356,844 (GRCm39)	N489S	possibly damaging	Het
Cramp1	A	G	17: 25,187,920 (GRCm39)	S1225P	probably damaging	Het
Dck	G	A	5: 88,913,166 (GRCm39)	G18R	probably benign	Het
Dnah5	A	T	15: 28,387,914 (GRCm39)	E3124D	probably benign	Het
Dync2i2	T	A	2: 29,923,953 (GRCm39)	T191S	probably benign	Het
Eogt	T	G	6: 97,090,839 (GRCm39)	L433F	probably damaging	Het
Fam135b	A	G	15: 71,334,744 (GRCm39)	S817P		Het
Fsip2	T	C	2: 82,812,374 (GRCm39)	Y2898H	possibly damaging	Het
Fzr1	T	C	10: 81,205,249 (GRCm39)	H249R	probably benign	Het
Gbp10	T	G	5: 105,366,861 (GRCm39)	Q457P	probably damaging	Het
Gin1	G	C	1: 97,710,819 (GRCm39)	L167F	probably damaging	Het
Gm14226	A	T	2: 154,866,843 (GRCm39)	I267F	probably damaging	Het
Gmnc	A	G	16: 26,781,642 (GRCm39)		probably null	Het
Hectd2	A	T	19: 36,576,402 (GRCm39)	I311F	probably damaging	Het
Heg1	A	G	16: 33,558,961 (GRCm39)	K1085E	probably benign	Het
Hmbs	G	A	9: 44,252,983 (GRCm39)	Q34*	probably null	Het
Hyal6	T	A	6: 24,734,151 (GRCm39)	M28K	probably benign	Het
Ifi27l2a	T	C	12: 103,405,678 (GRCm39)	V141A	possibly damaging	Het
Ift122	T	A	6: 115,867,492 (GRCm39)	I414N	probably damaging	Het
Iglv2	A	T	16: 19,079,434 (GRCm39)	V23E	probably damaging	Het
Itgax	A	T	7: 127,730,641 (GRCm39)	I120L	probably benign	Het
Kifc3	A	G	8: 95,853,317 (GRCm39)	I13T	probably benign	Het
Lmod3	T	C	6: 97,224,625 (GRCm39)	N399D	probably damaging	Het
Macf1	A	T	4: 123,365,326 (GRCm39)	I3145K	probably benign	Het
Map2k5	A	C	9: 63,201,006 (GRCm39)	I209S	probably damaging	Het
Mbd5	A	G	2: 49,141,388 (GRCm39)	E117G	probably damaging	Het
Milr1	A	G	11: 106,652,105 (GRCm39)	H172R	probably benign	Het
Myod1	A	C	7: 46,026,593 (GRCm39)	D166A		Het
Neb	C	T	2: 52,100,878 (GRCm39)	V4647M	possibly damaging	Het
Nek1	A	T	8: 61,574,055 (GRCm39)	D1101V	probably damaging	Het
Nlrp2	A	T	7: 5,330,572 (GRCm39)	V608D	probably benign	Het
Noc3l	G	A	19: 38,800,835 (GRCm39)	Q216*	probably null	Het
Nos1	G	C	5: 118,017,402 (GRCm39)	R255P	probably benign	Het
Nup160	T	A	2: 90,552,585 (GRCm39)		probably benign	Het
Nxt2	C	T	X: 141,020,747 (GRCm39)	A118V	possibly damaging	Het
Oat	C	T	7: 132,166,006 (GRCm39)	S193N	probably benign	Het
Oma1	A	G	4: 103,182,214 (GRCm39)		probably null	Het
Or12e13	G	T	2: 87,663,523 (GRCm39)	G47*	probably null	Het
Or1e16	T	A	11: 73,286,853 (GRCm39)		probably benign	Het
Or1j15	T	G	2: 36,458,988 (GRCm39)	F126C	probably benign	Het
Or6c206	A	G	10: 129,097,184 (GRCm39)	Y118C	probably damaging	Het
Or6c216	A	G	10: 129,678,482 (GRCm39)	V143A	probably damaging	Het
Os9	A	G	10: 126,933,918 (GRCm39)	S500P	possibly damaging	Het
Osbpl11	A	T	16: 33,047,660 (GRCm39)	N541I		Het
Pcnx4	A	G	12: 72,613,671 (GRCm39)	I539V	probably benign	Het
Ppfia3	T	A	7: 44,999,717 (GRCm39)		probably null	Het
Ppp1r3a	T	C	6: 14,722,098 (GRCm39)	K275E	probably benign	Het
Pten	A	G	19: 32,769,972 (GRCm39)	N63S	probably benign	Het
Rptor	A	G	11: 119,777,896 (GRCm39)	N1020S	probably benign	Het
Sall2	C	A	14: 52,550,673 (GRCm39)	D841Y	possibly damaging	Het
Sbno1	T	A	5: 124,519,762 (GRCm39)	H1172L	probably benign	Het
Scaf4	A	T	16: 90,027,054 (GRCm39)	L921Q	probably damaging	Het
Sec22c	C	A	9: 121,524,750 (GRCm39)	R11L	probably damaging	Het
Skint6	T	A	4: 113,034,173 (GRCm39)	D318V	probably damaging	Het
Slc22a28	T	C	19: 8,049,205 (GRCm39)	N348S	probably benign	Het
Slc44a2	G	T	9: 21,253,305 (GRCm39)	K77N	possibly damaging	Het
Smc1b	C	T	15: 84,950,431 (GRCm39)	V1198I	probably benign	Het
Spef2	A	T	15: 9,717,568 (GRCm39)	M316K	probably damaging	Het
Stra8	T	C	6: 34,911,016 (GRCm39)	Y215H	probably damaging	Het
Sv2a	G	T	3: 96,097,010 (GRCm39)	R445L	probably benign	Het
Tchp	A	T	5: 114,859,184 (GRCm39)	R493*	probably null	Het
Ttc13	G	A	8: 125,410,039 (GRCm39)	A391V	probably benign	Het
Unc13b	C	T	4: 43,176,186 (GRCm39)	T2338I	unknown	Het
Wac	A	G	18: 7,921,592 (GRCm39)	D576G	probably damaging	Het
Xdh	T	C	17: 74,222,688 (GRCm39)	N559S	probably benign	Het
Zscan20	A	T	4: 128,481,914 (GRCm39)	S583T	probably benign	Het

Other mutations in Sycp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00513:Sycp1	APN	3	102,748,278 (GRCm39)	missense	probably benign
IGL00833:Sycp1	APN	3	102,783,617 (GRCm39)	critical splice donor site	probably null
IGL01066:Sycp1	APN	3	102,827,950 (GRCm39)	missense	probably damaging	1.00
IGL01484:Sycp1	APN	3	102,823,183 (GRCm39)	missense	probably benign	0.01
IGL02139:Sycp1	APN	3	102,772,430 (GRCm39)	missense	probably benign	0.00
IGL02270:Sycp1	APN	3	102,803,259 (GRCm39)	missense	probably benign	0.12
IGL02347:Sycp1	APN	3	102,800,863 (GRCm39)	missense	probably benign	0.00
IGL02630:Sycp1	APN	3	102,786,080 (GRCm39)	splice site	probably benign
IGL02668:Sycp1	APN	3	102,727,847 (GRCm39)	splice site	probably benign
IGL02928:Sycp1	APN	3	102,726,134 (GRCm39)	utr 3 prime	probably benign
PIT4458001:Sycp1	UTSW	3	102,842,149 (GRCm39)	missense	probably benign	0.01
R0027:Sycp1	UTSW	3	102,803,226 (GRCm39)	missense	probably benign
R0282:Sycp1	UTSW	3	102,823,111 (GRCm39)	splice site	probably benign
R0462:Sycp1	UTSW	3	102,726,422 (GRCm39)	missense	possibly damaging	0.75
R0609:Sycp1	UTSW	3	102,806,165 (GRCm39)	splice site	probably null
R0837:Sycp1	UTSW	3	102,822,561 (GRCm39)	missense	probably benign	0.17
R1301:Sycp1	UTSW	3	102,827,938 (GRCm39)	missense	probably benign	0.02
R2408:Sycp1	UTSW	3	102,832,575 (GRCm39)	missense	probably damaging	1.00
R2449:Sycp1	UTSW	3	102,832,522 (GRCm39)	missense	probably benign	0.15
R2516:Sycp1	UTSW	3	102,752,382 (GRCm39)	missense	probably benign	0.09
R2880:Sycp1	UTSW	3	102,726,214 (GRCm39)	missense	probably damaging	0.99
R3410:Sycp1	UTSW	3	102,748,357 (GRCm39)	missense	possibly damaging	0.94
R3427:Sycp1	UTSW	3	102,783,666 (GRCm39)	missense	probably benign	0.00
R4538:Sycp1	UTSW	3	102,748,278 (GRCm39)	missense	probably benign
R4679:Sycp1	UTSW	3	102,829,778 (GRCm39)	critical splice acceptor site	probably null
R4707:Sycp1	UTSW	3	102,760,805 (GRCm39)	missense	possibly damaging	0.92
R4785:Sycp1	UTSW	3	102,760,805 (GRCm39)	missense	possibly damaging	0.92
R5017:Sycp1	UTSW	3	102,803,303 (GRCm39)	splice site	probably null
R5036:Sycp1	UTSW	3	102,727,916 (GRCm39)	missense	probably damaging	1.00
R5044:Sycp1	UTSW	3	102,752,370 (GRCm39)	missense	probably benign	0.03
R5070:Sycp1	UTSW	3	102,827,881 (GRCm39)	missense	probably damaging	0.97
R5079:Sycp1	UTSW	3	102,786,116 (GRCm39)	missense	possibly damaging	0.67
R5289:Sycp1	UTSW	3	102,841,569 (GRCm39)	missense	possibly damaging	0.85
R5393:Sycp1	UTSW	3	102,748,363 (GRCm39)	splice site	probably null
R5477:Sycp1	UTSW	3	102,726,206 (GRCm39)	missense	probably damaging	1.00
R5576:Sycp1	UTSW	3	102,726,218 (GRCm39)	missense	probably damaging	0.98
R5814:Sycp1	UTSW	3	102,803,213 (GRCm39)	missense	probably benign	0.03
R6291:Sycp1	UTSW	3	102,816,277 (GRCm39)	missense	probably damaging	1.00
R6460:Sycp1	UTSW	3	102,832,569 (GRCm39)	missense	probably damaging	1.00
R6527:Sycp1	UTSW	3	102,806,203 (GRCm39)	missense	probably benign	0.09
R6870:Sycp1	UTSW	3	102,842,919 (GRCm39)	missense	probably damaging	1.00
R6873:Sycp1	UTSW	3	102,748,296 (GRCm39)	missense	probably benign
R7037:Sycp1	UTSW	3	102,806,250 (GRCm39)	missense	possibly damaging	0.62
R7210:Sycp1	UTSW	3	102,760,808 (GRCm39)	missense	probably damaging	1.00
R7405:Sycp1	UTSW	3	102,832,543 (GRCm39)	missense	possibly damaging	0.72
R7604:Sycp1	UTSW	3	102,820,749 (GRCm39)	missense	probably damaging	0.98
R7733:Sycp1	UTSW	3	102,803,278 (GRCm39)	missense	probably benign	0.00
R7858:Sycp1	UTSW	3	102,806,273 (GRCm39)	missense	probably benign	0.09
R7909:Sycp1	UTSW	3	102,727,942 (GRCm39)	nonsense	probably null
R8109:Sycp1	UTSW	3	102,758,918 (GRCm39)	missense	probably benign	0.21
R8141:Sycp1	UTSW	3	102,842,885 (GRCm39)	missense	possibly damaging	0.73
R8289:Sycp1	UTSW	3	102,748,353 (GRCm39)	missense	probably benign	0.01
R8359:Sycp1	UTSW	3	102,727,909 (GRCm39)	missense	probably damaging	0.98
R8844:Sycp1	UTSW	3	102,772,421 (GRCm39)	missense	probably damaging	1.00
R9020:Sycp1	UTSW	3	102,783,653 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- GGGAAAGATAGTGAAAAGCTGTATTTT -3'
(R):5'- AGCCTTGATGTTTAGGAGAGGA -3'

Sequencing Primer
(F):5'- GACATCAAGTTGAACCATAC -3'
(R):5'- CCTTGATGTTTAGGAGAGGAGAGTG -3'

Posted On

2022-01-20