Mutagenetix > Incidental Mutation

Incidental Mutation 'R4659:Sf3a2'

386383

Institutional Source

Beutler Lab

Gene Symbol

Sf3a2

Ensembl Gene

ENSMUSG00000020211

Gene Name

splicing factor 3a, subunit 2

Synonyms

PRP11, 66kDa, Sap62, SFA66

MMRRC Submission

041919-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R4659 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

80634569-80640756 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 80639418 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 136 (I136T)

Ref Sequence

ENSEMBL: ENSMUSP00000117160 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020435] [ENSMUST00000036016] [ENSMUST00000036805] [ENSMUST00000147440] [ENSMUST00000148665] [ENSMUST00000151928] [ENSMUST00000181039] [ENSMUST00000181945]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000020435

SMART Domains

Protein: ENSMUSP00000020435
Gene: ENSMUSG00000020216

Domain	Start	End	E-Value	Type
low complexity region	52	77	N/A	INTRINSIC
Pfam:JSRP	79	138	1e-29	PFAM
low complexity region	145	158	N/A	INTRINSIC
low complexity region	179	192	N/A	INTRINSIC
low complexity region	205	230	N/A	INTRINSIC
low complexity region	273	284	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000036016

SMART Domains

Protein: ENSMUSP00000043153
Gene: ENSMUSG00000035262

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
low complexity region	38	52	N/A	INTRINSIC
Pfam:AMH_N	75	439	3e-133	PFAM
TGFB	456	554	8.57e-36	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000036805

SMART Domains

Protein: ENSMUSP00000042334
Gene: ENSMUSG00000035278

Domain	Start	End	E-Value	Type
PH	16	110	1.48e-7	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139461

Predicted Effect

probably benign
Transcript: ENSMUST00000147440

SMART Domains

Protein: ENSMUSP00000116478
Gene: ENSMUSG00000020211

Domain	Start	End	E-Value	Type
low complexity region	18	36	N/A	INTRINSIC
Blast:CactinC_cactus	41	67	1e-9	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000148665
AA Change: I136T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000117160
Gene: ENSMUSG00000020211
AA Change: I136T

Domain	Start	End	E-Value	Type
low complexity region	18	36	N/A	INTRINSIC
ZnF_U1	51	85	5.02e-9	SMART
ZnF_C2H2	54	78	1.23e1	SMART
CactinC_cactus	91	219	8.29e-35	SMART
low complexity region	300	318	N/A	INTRINSIC
low complexity region	320	420	N/A	INTRINSIC
low complexity region	423	452	N/A	INTRINSIC
low complexity region	459	484	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000151928
AA Change: I136T

PolyPhen 2 Score 0.951 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000114164
Gene: ENSMUSG00000020211
AA Change: I136T

Domain	Start	End	E-Value	Type
low complexity region	18	36	N/A	INTRINSIC
ZnF_U1	51	85	5.02e-9	SMART
ZnF_C2H2	54	78	1.23e1	SMART
CactinC_cactus	91	194	1.26e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000181039

SMART Domains

Protein: ENSMUSP00000137666
Gene: ENSMUSG00000020216

Domain	Start	End	E-Value	Type
low complexity region	92	117	N/A	INTRINSIC
Pfam:JSRP	118	179	1e-31	PFAM
low complexity region	185	198	N/A	INTRINSIC
low complexity region	219	232	N/A	INTRINSIC
low complexity region	245	270	N/A	INTRINSIC
low complexity region	313	324	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000181945

SMART Domains

Protein: ENSMUSP00000137960
Gene: ENSMUSG00000020216

Domain	Start	End	E-Value	Type
transmembrane domain	53	75	N/A	INTRINSIC

Meta Mutation Damage Score

0.8941

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

96% (74/77)

Allele List at MGI

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc9	C	A	6: 142,618,321 (GRCm39)		probably null	Het
Ankrd22	C	T	19: 34,102,968 (GRCm39)	V118I	probably damaging	Het
Aoc1	A	T	6: 48,883,010 (GRCm39)	E295D	probably benign	Het
Arap2	T	C	5: 62,811,469 (GRCm39)	N1114S	possibly damaging	Het
AU021092	C	G	16: 5,030,011 (GRCm39)	A335P	probably damaging	Het
Carhsp1	T	C	16: 8,482,129 (GRCm39)	T51A	probably benign	Het
Cdc42bpb	T	C	12: 111,306,325 (GRCm39)	D152G	probably damaging	Het
Cep70	T	A	9: 99,178,394 (GRCm39)	D497E	possibly damaging	Het
Chrm5	T	C	2: 112,310,102 (GRCm39)	N338S	probably benign	Het
Cldn8	G	A	16: 88,359,296 (GRCm39)	H210Y	probably benign	Het
Clhc1	T	A	11: 29,528,229 (GRCm39)	*586K	probably null	Het
Cplane1	G	T	15: 8,245,760 (GRCm39)		probably benign	Het
Dop1a	T	A	9: 86,384,085 (GRCm39)		probably benign	Het
Dync1h1	T	C	12: 110,595,201 (GRCm39)	F1371S	possibly damaging	Het
Eif6	A	G	2: 155,668,101 (GRCm39)	I46T	probably damaging	Het
Esco2	G	A	14: 66,064,035 (GRCm39)	T383M	possibly damaging	Het
Exoc8	T	C	8: 125,624,271 (GRCm39)	D32G	probably damaging	Het
Fam149b	G	T	14: 20,417,941 (GRCm39)	S216I	probably benign	Het
Fam219a	T	C	4: 41,521,645 (GRCm39)	D87G	probably null	Het
Fbxw26	A	T	9: 109,573,939 (GRCm39)	V71D	probably damaging	Het
Gabra4	T	A	5: 71,798,487 (GRCm39)	K164M	probably damaging	Het
Gm57858	T	C	3: 36,080,103 (GRCm39)	D218G	possibly damaging	Het
Gm8603	G	A	17: 13,737,290 (GRCm39)		noncoding transcript	Het
Gnmt	A	G	17: 47,036,892 (GRCm39)	F239S	probably damaging	Het
Gpsm1	G	A	2: 26,209,843 (GRCm39)		probably benign	Het
Jam2	G	A	16: 84,609,840 (GRCm39)	V151M	probably damaging	Het
Kcnj1	A	T	9: 32,305,444 (GRCm39)	D2V	probably benign	Het
Limch1	C	T	5: 67,184,900 (GRCm39)	R797C	probably damaging	Het
Lrrc9	T	A	12: 72,517,038 (GRCm39)	F597I	probably damaging	Het
Lrriq3	T	A	3: 154,835,090 (GRCm39)	I275N	possibly damaging	Het
Mcoln1	T	A	8: 3,560,840 (GRCm39)	S387R	probably damaging	Het
Mgst3	T	A	1: 167,204,848 (GRCm39)	Q58L	probably damaging	Het
Mical1	G	A	10: 41,362,932 (GRCm39)		probably benign	Het
Mmp3	C	A	9: 7,453,673 (GRCm39)	D431E	probably benign	Het
Mx1	T	C	16: 97,256,439 (GRCm39)		probably null	Het
Myo7a	A	G	7: 97,734,673 (GRCm39)	L607P	probably damaging	Het
Myt1l	A	G	12: 29,899,456 (GRCm39)	N153D	probably damaging	Het
Nfu1	A	T	6: 86,996,408 (GRCm39)	T120S	probably damaging	Het
Nhlrc2	T	C	19: 56,564,699 (GRCm39)	V341A	possibly damaging	Het
Notch1	T	C	2: 26,360,901 (GRCm39)	E1148G	probably damaging	Het
Nqo1	C	T	8: 108,117,676 (GRCm39)		probably null	Het
Nwd1	T	A	8: 73,421,949 (GRCm39)	D998E	probably benign	Het
Or8k18	G	A	2: 86,085,357 (GRCm39)	Q227*	probably null	Het
Oxct2a	T	C	4: 123,216,473 (GRCm39)	I303V	probably benign	Het
Parp10	A	T	15: 76,127,185 (GRCm39)	D58E	probably damaging	Het
Pcdha6	T	A	18: 37,102,292 (GRCm39)	V495E	probably damaging	Het
Pitrm1	T	A	13: 6,603,218 (GRCm39)	S88R	probably benign	Het
Pxdn	T	C	12: 30,044,552 (GRCm39)	V510A	probably benign	Het
Ranbp17	T	A	11: 33,216,288 (GRCm39)	D820V	probably damaging	Het
Sec24c	G	T	14: 20,733,212 (GRCm39)	G180C	probably damaging	Het
Serpina3n	T	C	12: 104,379,752 (GRCm39)	S382P	probably benign	Het
Sestd1	A	T	2: 77,042,843 (GRCm39)	M237K	probably null	Het
Sh3tc2	A	G	18: 62,107,580 (GRCm39)	Y197C	probably benign	Het
Speer4b	T	C	5: 27,702,893 (GRCm39)	K204E	probably benign	Het
Speer4f1	A	C	5: 17,681,221 (GRCm39)	E33A	possibly damaging	Het
Sspo	T	A	6: 48,461,147 (GRCm39)	D3529E	probably damaging	Het
Stard13	T	C	5: 150,986,253 (GRCm39)	D419G	probably benign	Het
Tg	A	G	15: 66,545,769 (GRCm39)	S164G	possibly damaging	Het
Thap12	A	G	7: 98,359,298 (GRCm39)		probably benign	Het
Thsd1	C	A	8: 22,749,314 (GRCm39)	Y667*	probably null	Het
Tnks	A	C	8: 35,316,465 (GRCm39)	Y885D	possibly damaging	Het
Ttll3	A	G	6: 113,391,102 (GRCm39)	I896V	probably benign	Het
Txnip	T	G	3: 96,466,743 (GRCm39)	F190C	probably damaging	Het
Urb1	T	C	16: 90,573,017 (GRCm39)	D1005G	probably damaging	Het
Usp3	T	C	9: 66,434,352 (GRCm39)		probably null	Het
Usp54	G	T	14: 20,615,060 (GRCm39)	Q794K	probably damaging	Het
Xrn2	A	G	2: 146,903,394 (GRCm39)	Q798R	probably benign	Het
Zfp189	A	G	4: 49,530,342 (GRCm39)	I482V	probably benign	Het
Zfp28	A	G	7: 6,396,506 (GRCm39)	N314D	probably benign	Het
Zmym4	A	G	4: 126,842,221 (GRCm39)		probably null	Het

Other mutations in Sf3a2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01717:Sf3a2	APN	10	80,640,526 (GRCm39)	nonsense	probably null
IGL02997:Sf3a2	APN	10	80,639,454 (GRCm39)	missense	probably damaging	1.00
R0470:Sf3a2	UTSW	10	80,640,388 (GRCm39)	unclassified	probably benign
R1436:Sf3a2	UTSW	10	80,640,040 (GRCm39)	unclassified	probably benign
R1437:Sf3a2	UTSW	10	80,640,040 (GRCm39)	unclassified	probably benign
R2233:Sf3a2	UTSW	10	80,638,663 (GRCm39)	missense	probably benign	0.05
R2234:Sf3a2	UTSW	10	80,638,663 (GRCm39)	missense	probably benign	0.05
R3871:Sf3a2	UTSW	10	80,640,527 (GRCm39)	unclassified	probably benign
R4116:Sf3a2	UTSW	10	80,637,175 (GRCm39)	missense	probably damaging	0.98
R4946:Sf3a2	UTSW	10	80,639,947 (GRCm39)	unclassified	probably benign
R5081:Sf3a2	UTSW	10	80,640,275 (GRCm39)	unclassified	probably benign
R5618:Sf3a2	UTSW	10	80,640,410 (GRCm39)	unclassified	probably benign
R6039:Sf3a2	UTSW	10	80,637,297 (GRCm39)	missense	probably damaging	1.00
R6039:Sf3a2	UTSW	10	80,637,297 (GRCm39)	missense	probably damaging	1.00
R7925:Sf3a2	UTSW	10	80,640,271 (GRCm39)	unclassified	probably benign
R7930:Sf3a2	UTSW	10	80,640,271 (GRCm39)	unclassified	probably benign
R8118:Sf3a2	UTSW	10	80,639,474 (GRCm39)	missense	probably damaging	1.00
R8170:Sf3a2	UTSW	10	80,639,131 (GRCm39)	splice site	probably null
R8757:Sf3a2	UTSW	10	80,640,138 (GRCm39)	missense	unknown
R8785:Sf3a2	UTSW	10	80,640,271 (GRCm39)	unclassified	probably benign
R8874:Sf3a2	UTSW	10	80,640,271 (GRCm39)	unclassified	probably benign
R9111:Sf3a2	UTSW	10	80,640,271 (GRCm39)	unclassified	probably benign
R9292:Sf3a2	UTSW	10	80,640,560 (GRCm39)	missense	unknown
R9575:Sf3a2	UTSW	10	80,640,271 (GRCm39)	unclassified	probably benign
R9663:Sf3a2	UTSW	10	80,637,309 (GRCm39)	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- TGAGGAACCCTGTTCTGTTG -3'
(R):5'- AAAGTCAGAGGCTGCAGCAC -3'

Sequencing Primer
(F):5'- GGAACCCTGTTCTGTTGTGCAC -3'
(R):5'- GATACACAGACAGCTGAATTTAGC -3'

Posted On

2016-05-20