Mutagenetix > Incidental Mutation

Incidental Mutation 'R1544:Spns2'

172043

Institutional Source

Beutler Lab

Gene Symbol

Spns2

Ensembl Gene

ENSMUSG00000040447

Gene Name

spinster homolog 2

Synonyms

MMRRC Submission

039583-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1544 (G1)

Quality Score

199

Status

Validated

Chromosome

Chromosomal Location

72451638-72489904 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 72456367 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 427 (I427N)

Ref Sequence

ENSEMBL: ENSMUSP00000044418 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000045303] [ENSMUST00000045633]

AlphaFold

Q91VM4

Predicted Effect

probably benign
Transcript: ENSMUST00000045303
AA Change: I427N

PolyPhen 2 Score 0.300 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000044418
Gene: ENSMUSG00000040447
AA Change: I427N

Domain	Start	End	E-Value	Type
low complexity region	5	53	N/A	INTRINSIC
Pfam:Sugar_tr	104	308	7.6e-16	PFAM
Pfam:OATP	106	427	7.2e-13	PFAM
Pfam:MFS_1	108	476	2.7e-37	PFAM
transmembrane domain	506	528	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000045633

SMART Domains

Protein: ENSMUSP00000044827
Gene: ENSMUSG00000040463

Domain	Start	End	E-Value	Type
low complexity region	7	19	N/A	INTRINSIC
Pfam:DNA_pol_phi	70	835	1.2e-194	PFAM
low complexity region	839	852	N/A	INTRINSIC
low complexity region	1080	1090	N/A	INTRINSIC
low complexity region	1109	1122	N/A	INTRINSIC
low complexity region	1259	1269	N/A	INTRINSIC
low complexity region	1314	1329	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126452

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129274

Predicted Effect

unknown
Transcript: ENSMUST00000144940
AA Change: I41N

SMART Domains

Protein: ENSMUSP00000120722
Gene: ENSMUSG00000040447
AA Change: I41N

Domain	Start	End	E-Value	Type
transmembrane domain	13	32	N/A	INTRINSIC
transmembrane domain	37	59	N/A	INTRINSIC
transmembrane domain	80	102	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147418

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150491

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152894

Meta Mutation Damage Score

0.1711

Coding Region Coverage

1x: 98.9%
3x: 97.9%
10x: 94.7%
20x: 86.9%

Validation Efficiency

99% (114/115)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a transporter of sphingosine 1-phosphate, a secreted lipid that is important in cardiovascular, immunological, and neural development. Defects in this gene are a cause of early onset progressive hearing loss. [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit symblepharon and impaired egress of T and B cells from the thymus and bone marrow, respectively. Mice homozygous for a different knock-out allele exhibit abnormal immune system, abnormal eye morphology and absent pinna reflex. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 111 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930578C19Rik	A	C	X: 18,420,462	L285V	possibly damaging	Het
4931406B18Rik	A	G	7: 43,498,119	I182T	possibly damaging	Het
4933406P04Rik	A	G	10: 20,311,359		probably benign	Het
4933425L06Rik	A	T	13: 105,109,621	H230L	probably benign	Het
A730018C14Rik	A	G	12: 112,415,490		noncoding transcript	Het
Aacs	A	T	5: 125,516,330	I666F	possibly damaging	Het
Abcb9	C	T	5: 124,083,631	V227I	probably benign	Het
Abcd3	T	C	3: 121,784,473	Q168R	probably benign	Het
Adamts4	A	G	1: 171,252,742	Q288R	probably benign	Het
Atad2	G	A	15: 58,103,364	A611V	probably damaging	Het
Aup1	T	C	6: 83,055,206	V118A	possibly damaging	Het
Bend7	T	A	2: 4,763,311		probably benign	Het
Brd4	A	G	17: 32,198,672		probably benign	Het
C4b	C	A	17: 34,738,967	R580L	probably benign	Het
Cct8	G	T	16: 87,491,454		probably benign	Het
Cilp	T	C	9: 65,275,845	Y344H	probably benign	Het
Clic6	A	T	16: 92,492,073		probably benign	Het
Colgalt2	T	C	1: 152,484,952	S247P	probably damaging	Het
Csf2rb	G	T	15: 78,340,755	A212S	probably benign	Het
Csmd3	A	C	15: 47,611,898		probably null	Het
Cyp26c1	A	G	19: 37,690,945	D366G	probably benign	Het
Dhx33	A	G	11: 70,999,528	S222P	probably damaging	Het
Dhx40	T	A	11: 86,806,553	I63F	possibly damaging	Het
Dlgap2	T	A	8: 14,829,861		probably null	Het
Dnah7b	T	A	1: 46,066,797	D20E	unknown	Het
Dnase2b	C	A	3: 146,584,557	A220S	probably benign	Het
Dock10	T	C	1: 80,592,635	E362G	probably benign	Het
Ect2l	C	T	10: 18,168,434	V226I	probably benign	Het
Epha10	C	A	4: 124,885,596	N78K	probably damaging	Het
Epha3	A	G	16: 63,773,053	V224A	probably damaging	Het
Fam126a	A	T	5: 23,965,141	D403E	probably benign	Het
Fam208b	A	T	13: 3,590,413	H241Q	possibly damaging	Het
Fcgr4	C	A	1: 171,019,954	D40E	probably damaging	Het
Fer1l4	T	C	2: 156,045,633	M548V	probably benign	Het
Flii	C	T	11: 60,719,692		probably null	Het
Flnc	A	T	6: 29,444,080	Y631F	probably benign	Het
Gm13101	T	C	4: 143,966,062	D123G	probably benign	Het
Gm14685	G	T	X: 73,127,655	G218C	probably damaging	Het
Gm4788	A	T	1: 139,736,870	C484S	probably damaging	Het
Gm6871	A	C	7: 41,546,090		probably null	Het
Gtf2ird1	A	T	5: 134,358,918	S1028T	possibly damaging	Het
Hydin	A	G	8: 110,574,854	H3739R	probably benign	Het
Iqcg	A	T	16: 33,045,525	N149K	probably benign	Het
Iqgap3	A	G	3: 88,098,893	D537G	probably benign	Het
Itih2	T	G	2: 10,105,214	D576A	probably benign	Het
Kcmf1	T	C	6: 72,848,229	T243A	probably benign	Het
Kif1a	A	G	1: 93,074,948		probably benign	Het
Klf10	C	T	15: 38,296,786	G337S	probably damaging	Het
Krt31	T	C	11: 100,047,873	N298S	possibly damaging	Het
Lmnb1	A	G	18: 56,749,751	E556G	probably benign	Het
Mael	A	T	1: 166,202,290	S354T	probably benign	Het
Mast3	T	C	8: 70,786,172	D496G	probably damaging	Het
Med12l	A	G	3: 59,265,240	T1806A	possibly damaging	Het
Mms19	A	G	19: 41,955,821		probably null	Het
Moap1	A	T	12: 102,743,245	M15K	possibly damaging	Het
Mpv17l	G	T	16: 13,946,819	W70L	probably damaging	Het
Muc4	G	C	16: 32,753,919	R1265P	probably benign	Het
Myo7b	T	C	18: 31,994,909	I577V	probably benign	Het
Myo9b	T	A	8: 71,290,976	L227Q	probably damaging	Het
Myom2	T	C	8: 15,104,059		probably benign	Het
Naip6	C	A	13: 100,316,475	R26L	probably benign	Het
Nbea	T	C	3: 56,058,827	T405A	probably damaging	Het
Nrp2	T	A	1: 62,762,904	I502N	probably damaging	Het
Nufip2	G	A	11: 77,691,907	E216K	possibly damaging	Het
Oaf	A	G	9: 43,222,633	Y264H	probably damaging	Het
Olfr1023	T	C	2: 85,887,271	L157P	probably damaging	Het
Olfr643	A	G	7: 104,059,224	V126A	probably damaging	Het
Olfr815	A	T	10: 129,902,424	C95*	probably null	Het
Pax1	T	C	2: 147,368,401	V352A	probably damaging	Het
Pkd1l2	TGGG	TGG	8: 117,038,235		probably null	Het
Plxna3	G	A	X: 74,340,166		probably null	Het
Pnpla3	T	C	15: 84,181,046	V347A	probably benign	Het
Ppl	T	A	16: 5,102,597	K350*	probably null	Het
Prb1	C	A	6: 132,209,460		probably null	Het
Prb1	T	A	6: 132,209,461		probably null	Het
Ptpn11	G	A	5: 121,137,511	H540Y	probably benign	Het
Ptprz1	C	A	6: 23,000,748	H946N	possibly damaging	Het
Rad51b	A	G	12: 79,302,543	E51G	possibly damaging	Het
Rin2	T	C	2: 145,858,446	V181A	probably damaging	Het
Rnf157	T	A	11: 116,354,362		probably null	Het
Rnf207	A	G	4: 152,313,871		probably benign	Het
Ror1	A	T	4: 100,441,986	K852M	probably damaging	Het
Sbp	T	A	17: 23,945,069	I102K	probably benign	Het
Scaf8	T	C	17: 3,145,154	I33T	probably damaging	Het
Scn5a	C	T	9: 119,486,633	V1670I	probably damaging	Het
Serhl	C	T	15: 83,105,676	T42M	probably damaging	Het
Sin3a	A	G	9: 57,103,997		probably benign	Het
Slc12a2	A	G	18: 57,879,302	S166G	probably benign	Het
Slc15a4	G	A	5: 127,603,768	H396Y	probably benign	Het
Slc2a7	A	T	4: 150,154,686	N123Y	probably damaging	Het
Smpd3	G	A	8: 106,265,567	T118M	possibly damaging	Het
Ssmem1	T	A	6: 30,519,651	S112T	probably damaging	Het
Stard10	A	T	7: 101,344,026	D190V	probably damaging	Het
Stil	A	T	4: 115,023,852	K531M	probably damaging	Het
Strc	T	C	2: 121,372,738		probably null	Het
Svil	T	A	18: 5,046,817	I21N	possibly damaging	Het
Syt11	T	C	3: 88,748,803	M14V	probably benign	Het
Tg	A	T	15: 66,705,232	Q1468L	probably benign	Het
Tjp1	A	G	7: 65,302,921	V1555A	probably benign	Het
Tmprss11d	A	C	5: 86,338,799	S77R	probably damaging	Het
Tsnaxip1	A	G	8: 105,827,751		probably benign	Het
Tyr	C	A	7: 87,492,706	L138F	probably damaging	Het
Ubash3b	A	G	9: 41,016,605	V469A	probably damaging	Het
Ugt8a	T	C	3: 125,915,449	Y4C	probably benign	Het
Vmn1r201	A	T	13: 22,474,798	T61S	probably benign	Het
Vmn1r204	A	G	13: 22,556,295	H32R	probably benign	Het
Vmn1r228	T	A	17: 20,777,023	I78L	probably benign	Het
Wdr90	T	C	17: 25,849,310	D1348G	possibly damaging	Het
Zfp563	T	A	17: 33,105,213	C261S	probably benign	Het
Zfp809	T	A	9: 22,235,099	L28Q	probably damaging	Het
Znrf3	T	A	11: 5,289,066	Q99L	probably damaging	Het

Other mutations in Spns2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01733:Spns2	APN	11	72456510	missense	possibly damaging	0.79
IGL01804:Spns2	APN	11	72457304	missense	possibly damaging	0.89
elderly	UTSW	11	72456370	critical splice acceptor site	probably null
homely	UTSW	11	72456860	missense	probably damaging	1.00
whistler	UTSW	11	72458687	nonsense	probably null
Wrinkled	UTSW	11	72456878	missense	possibly damaging	0.81
R0883:Spns2	UTSW	11	72454397	missense	probably damaging	1.00
R1696:Spns2	UTSW	11	72456347	missense	probably benign	0.25
R2046:Spns2	UTSW	11	72459040	missense	possibly damaging	0.49
R2164:Spns2	UTSW	11	72458671	missense	possibly damaging	0.82
R2259:Spns2	UTSW	11	72457268	missense	probably benign	0.35
R4209:Spns2	UTSW	11	72454186	missense	probably benign	0.07
R5285:Spns2	UTSW	11	72489479	missense	possibly damaging	0.92
R6883:Spns2	UTSW	11	72456370	critical splice acceptor site	probably null
R6990:Spns2	UTSW	11	72489621	missense	probably benign	0.08
R7221:Spns2	UTSW	11	72456916	missense	probably benign	0.43
R7227:Spns2	UTSW	11	72458687	nonsense	probably null
R7243:Spns2	UTSW	11	72456860	missense	probably damaging	1.00
R7390:Spns2	UTSW	11	72456878	missense	possibly damaging	0.81
R7699:Spns2	UTSW	11	72489617	nonsense	probably null
R7700:Spns2	UTSW	11	72489617	nonsense	probably null
R8042:Spns2	UTSW	11	72454177	missense	possibly damaging	0.46
R8155:Spns2	UTSW	11	72456568	missense	possibly damaging	0.46
R8553:Spns2	UTSW	11	72457227	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCCCAGCAGCAAGTACTGCTTATTC -3'
(R):5'- ACAGCCTCATCTTTGGAGCCATTAC -3'

Sequencing Primer
(F):5'- GCAGCAAGTACTGCTTATTCTTCAC -3'
(R):5'- CAACGTGCTGACCCATTG -3'

Posted On

2014-04-13