Mutagenetix > Incidental Mutation

Incidental Mutation 'R8141:Sycp1'

632525

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: 0.583) question?

Stock #

R8141 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

102818499-102936100 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 102935569 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Glutamic Acid at position 28 (A28E)

Ref Sequence

ENSEMBL: ENSMUSP00000029448 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029448] [ENSMUST00000058899] [ENSMUST00000196988] [ENSMUST00000199930]

AlphaFold

Q62209

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029448
AA Change: A28E

PolyPhen 2 Score 0.732 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000029448
Gene: ENSMUSG00000027855
AA Change: A28E

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

Predicted Effect

probably benign
Transcript: ENSMUST00000058899

SMART Domains

Protein: ENSMUSP00000052557
Gene: ENSMUSG00000048938

Domain	Start	End	E-Value	Type
Blast:HOLI	2	47	5e-9	BLAST
ZnF_C4	119	190	2.51e-36	SMART
HOLI	289	474	1.74e-21	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000196988
AA Change: A28E

PolyPhen 2 Score 0.732 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000143651
Gene: ENSMUSG00000027855
AA Change: A28E

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

Predicted Effect

unknown
Transcript: ENSMUST00000199930
AA Change: A28E

SMART Domains

Protein: ENSMUSP00000143493
Gene: ENSMUSG00000027855
AA Change: A28E

Domain	Start	End	E-Value	Type
Pfam:SCP-1	28	95	2e-33	PFAM
Pfam:SCP-1	93	182	9.8e-53	PFAM

Coding Region Coverage

1x: 99.8%
3x: 99.6%
10x: 98.3%
20x: 90.7%

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017B05Rik	T	C	9: 57,258,405	T229A	probably benign	Het
4930438A08Rik	A	G	11: 58,286,585	E40G		Het
Actn2	T	C	13: 12,288,630	D428G	probably damaging	Het
Arl14epl	C	A	18: 46,926,343	N8K	probably benign	Het
Bend7	T	C	2: 4,752,825	V226A	probably benign	Het
C1s1	A	T	6: 124,531,362	L556Q	probably damaging	Het
Casr	T	C	16: 36,494,811	K966E	probably damaging	Het
Ccm2l	T	C	2: 153,070,871	L110P	probably damaging	Het
Cdhr4	G	A	9: 107,996,792	R59H		Het
Celf3	C	A	3: 94,488,543	N410K	probably damaging	Het
Cpne6	T	C	14: 55,512,609	C66R	possibly damaging	Het
Cyp2f2	G	A	7: 27,129,253	V183I	probably benign	Het
Eln	CTCCAGCTCCGAT	C	5: 134,729,149		probably benign	Het
Fam53b	A	C	7: 132,760,029	V90G	probably damaging	Het
Fat3	T	A	9: 15,997,066	I2547F	possibly damaging	Het
Foxk1	A	G	5: 142,453,961	Y524C	probably damaging	Het
Gm884	T	C	11: 103,621,029	T38A	unknown	Het
Gpr87	A	G	3: 59,179,599	S162P	probably damaging	Het
Grasp	T	A	15: 101,231,909	C358S	possibly damaging	Het
Ifi204	A	G	1: 173,755,623	V343A	possibly damaging	Het
Igsf10	A	G	3: 59,330,528	L744P	probably damaging	Het
Iqub	T	A	6: 24,491,609	K359N	probably benign	Het
Kdm3b	A	T	18: 34,828,546	K1459*	probably null	Het
Kirrel	C	T	3: 87,086,428	W507*	probably null	Het
Klra17	T	C	6: 129,872,329	D94G	probably damaging	Het
Llgl1	G	C	11: 60,710,316	E693D	probably benign	Het
Lypd4	A	T	7: 24,864,829	D201E	possibly damaging	Het
Nin	A	G	12: 70,030,021	S1794P		Het
Olfr430	T	C	1: 174,069,922	L208P	probably damaging	Het
Oog2	T	C	4: 144,194,207	L70P	probably damaging	Het
Pacsin1	G	T	17: 27,707,060	R282S	possibly damaging	Het
Pcdhb9	T	A	18: 37,402,308	Y452N	probably damaging	Het
Pdgfra	T	C	5: 75,177,726	V547A	possibly damaging	Het
Plcb4	T	C	2: 135,939,249	F209L	probably damaging	Het
Pnpla6	T	C	8: 3,521,384	S158P	probably benign	Het
Prlhr	C	G	19: 60,467,309	R273P	probably damaging	Het
Prss41	G	A	17: 23,837,633	P196L	probably damaging	Het
Ptpn22	A	G	3: 103,886,327	E598G	possibly damaging	Het
Rasal2	T	C	1: 157,164,670	D569G	possibly damaging	Het
Sf3b3	A	C	8: 110,820,851	M715R	possibly damaging	Het
Ska1	T	C	18: 74,206,836	N13S	probably benign	Het
Spocd1	A	C	4: 129,929,704	E98A		Het
Syf2	C	T	4: 134,936,871	R199C	probably damaging	Het
Syne2	A	G	12: 76,061,668	D942G	possibly damaging	Het
Tmem63a	A	G	1: 180,974,211	T764A	probably benign	Het
Ttf1	C	T	2: 29,067,226	Q503*	probably null	Het
Usp13	T	C	3: 32,894,876	V454A	possibly damaging	Het
Usp47	A	G	7: 112,053,265	T50A	possibly damaging	Het
Wdr66	T	G	5: 123,286,430	V726G	possibly damaging	Het
Zadh2	T	C	18: 84,094,526	L109P	probably benign	Het
Zfyve26	A	T	12: 79,268,557	C1382S	possibly 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
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
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
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'- ACATACAAAGTGTAAGGCATGC -3'
(R):5'- ACGTACACACCTCTGTCACG -3'

Sequencing Primer
(F):5'- ACAAAGTGTAAGGCATGCTTTTC -3'
(R):5'- TGCAGGCTTTCACCGTG -3'

Posted On

2020-06-30