Mutagenetix > Incidental Mutation

Incidental Mutation 'R7243:Spns2'

563374

Institutional Source

Beutler Lab

Gene Symbol

Spns2

Ensembl Gene

ENSMUSG00000040447

Gene Name

SPNS lysolipid transporter 2, sphingosine-1-phosphate

Synonyms

MMRRC Submission

045307-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7243 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

72342464-72380730 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 72347686 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 335 (W335R)

Ref Sequence

ENSEMBL: ENSMUSP00000044418 (fasta)

Gene Model

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

AlphaFold

Q91VM4

Predicted Effect

probably damaging
Transcript: ENSMUST00000045303
AA Change: W335R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000044418
Gene: ENSMUSG00000040447
AA Change: W335R

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: ENSMUST00000144940

SMART Domains

Protein: ENSMUSP00000120722
Gene: ENSMUSG00000040447

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

Meta Mutation Damage Score

0.8626

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

99% (73/74)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acap1	G	A	11: 69,781,297 (GRCm39)	H103Y	probably benign	Het
Adamdec1	A	G	14: 68,809,203 (GRCm39)	M253T	probably benign	Het
Alox15	C	A	11: 70,241,540 (GRCm39)	G114C	probably null	Het
Aox3	G	T	1: 58,177,466 (GRCm39)	G227V	unknown	Het
Atp8a2	A	T	14: 59,885,291 (GRCm39)	N1144K	probably benign	Het
Cacna1c	C	T	6: 118,614,690 (GRCm39)		probably null	Het
Cog6	A	T	3: 52,909,736 (GRCm39)	W314R	probably damaging	Het
Col5a2	A	G	1: 45,415,320 (GRCm39)	I1473T	probably benign	Het
Csmd1	T	A	8: 15,965,357 (GRCm39)	D3218V	probably damaging	Het
Cyp3a11	A	G	5: 145,795,613 (GRCm39)	M446T	probably damaging	Het
Dhps	A	G	8: 85,801,567 (GRCm39)	Y340C	probably benign	Het
Dnah7b	A	G	1: 46,122,914 (GRCm39)	N108S	probably benign	Het
Dnajb1	C	T	8: 84,337,393 (GRCm39)	P323L	probably damaging	Het
Dspp	TGACAGCAGTGACAGCAGCGACAGCAGCGACAGCAGTGACAGCAGCGACAGCAGCGACAGCAGTGACAGCAGCGACAGCAGCAACAGCAGTGACAGCAG	TGACAGCAGTGACAGCAGCGACAGCAGCGACAGCAGTGACAGCAGCGACAGCAGCAACAGCAGTGACAGCAG	5: 104,326,227 (GRCm39)		probably benign	Het
Dync2h1	G	T	9: 7,102,405 (GRCm39)	T2665K	possibly damaging	Het
Etv1	C	T	12: 38,907,045 (GRCm39)	S349L	probably benign	Het
Fam171a1	A	T	2: 3,119,653 (GRCm39)	T21S	probably benign	Het
Fbh1	T	A	2: 11,756,336 (GRCm39)	T749S	probably benign	Het
Fcho2	T	C	13: 98,891,724 (GRCm39)	D346G	possibly damaging	Het
Fcrl5	A	G	3: 87,349,552 (GRCm39)	H109R	probably benign	Het
Fstl1	A	G	16: 37,647,088 (GRCm39)	S153G	probably benign	Het
Fyb1	T	C	15: 6,673,180 (GRCm39)	F605L	probably benign	Het
Gcat	T	A	15: 78,921,063 (GRCm39)	M363K	possibly damaging	Het
Gm10604	T	C	4: 11,980,113 (GRCm39)	T64A	unknown	Het
Grin2d	A	G	7: 45,515,552 (GRCm39)	L147P	probably damaging	Het
Ift88	A	T	14: 57,667,993 (GRCm39)		probably null	Het
Ighg1	A	T	12: 113,294,066 (GRCm39)	C26S		Het
Ing2	A	G	8: 48,127,574 (GRCm39)	S48P	probably damaging	Het
Kat6a	C	T	8: 23,428,791 (GRCm39)	T1382I	probably benign	Het
Kdm1a	A	G	4: 136,279,265 (GRCm39)	V765A	probably damaging	Het
Klk1b26	T	C	7: 43,665,691 (GRCm39)	S168P	not run	Het
Klk1b26	A	G	7: 43,666,337 (GRCm39)	N260S	probably damaging	Het
Lama3	G	A	18: 12,552,902 (GRCm39)	G438D	probably damaging	Het
Larp6	T	A	9: 60,620,569 (GRCm39)	D27E	probably benign	Het
Lrba	T	A	3: 86,658,823 (GRCm39)		probably null	Het
Lrig2	A	T	3: 104,404,883 (GRCm39)		probably null	Het
Megf9	T	C	4: 70,353,708 (GRCm39)	E366G	probably benign	Het
Mob1b	T	A	5: 88,891,304 (GRCm39)	D52E	probably damaging	Het
Ndufb3	A	T	1: 58,630,282 (GRCm39)	H11L	unknown	Het
Odc1	T	G	12: 17,600,058 (GRCm39)	Y407*	probably null	Het
Ogfr	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	2: 180,237,059 (GRCm39)		probably benign	Het
Opa1	A	G	16: 29,405,814 (GRCm39)	I126M	probably benign	Het
Or2t47	T	C	11: 58,442,227 (GRCm39)	I279M	probably damaging	Het
Or3a1b	T	A	11: 74,012,559 (GRCm39)	V148E	probably damaging	Het
Or51a10	A	G	7: 103,698,962 (GRCm39)	Y200H	probably damaging	Het
Or51f5	A	T	7: 102,430,865 (GRCm39)	T61S	probably benign	Het
Pcca	A	G	14: 123,114,186 (GRCm39)	H633R	probably benign	Het
Pcdhb22	A	G	18: 37,653,685 (GRCm39)	R461G	probably benign	Het
Pcf11	A	T	7: 92,309,268 (GRCm39)	D647E	probably damaging	Het
Plscr1l1	A	G	9: 92,225,726 (GRCm39)	Y16C	probably damaging	Het
Plxnd1	T	A	6: 115,949,468 (GRCm39)	I773F	probably benign	Het
Prl8a1	A	T	13: 27,766,086 (GRCm39)	L3Q	probably damaging	Het
Psg17	C	A	7: 18,552,640 (GRCm39)	G212C	probably damaging	Het
Ptbp2	G	T	3: 119,546,761 (GRCm39)	N40K	possibly damaging	Het
Ptprj	T	C	2: 90,276,765 (GRCm39)	H1102R	probably damaging	Het
Rbfox3	T	C	11: 118,404,100 (GRCm39)	Y33C	probably damaging	Het
Ros1	T	A	10: 51,999,477 (GRCm39)	N1158Y	probably damaging	Het
Rpgrip1l	T	C	8: 91,996,751 (GRCm39)	I710V	probably benign	Het
Scn9a	A	G	2: 66,370,874 (GRCm39)	F569L	probably damaging	Het
Slc12a4	A	T	8: 106,680,552 (GRCm39)	M190K	probably damaging	Het
Slc22a20	G	A	19: 6,021,599 (GRCm39)	R468C	probably damaging	Het
Slc45a2	T	A	15: 11,023,436 (GRCm39)	Y347N	possibly damaging	Het
Slc4a10	A	G	2: 62,134,206 (GRCm39)	Y974C	probably damaging	Het
Snap47	A	G	11: 59,319,548 (GRCm39)	S197P	probably benign	Het
Snph	T	C	2: 151,436,173 (GRCm39)	S252G	probably damaging	Het
Thnsl1	A	G	2: 21,217,658 (GRCm39)	I471V	probably damaging	Het
Tmprss11f	C	A	5: 86,677,975 (GRCm39)	G265C	probably damaging	Het
Tnn	C	T	1: 159,934,687 (GRCm39)	R1242H	probably benign	Het
Tsc2	T	C	17: 24,818,604 (GRCm39)	R1412G	probably benign	Het
Tsc22d2	G	T	3: 58,323,884 (GRCm39)	V259F	unknown	Het
Ttll13	A	C	7: 79,903,911 (GRCm39)	K280Q	probably damaging	Het
Wls	A	T	3: 159,615,402 (GRCm39)	I306F	possibly damaging	Het
Zfp566	A	G	7: 29,777,701 (GRCm39)	V160A	probably benign	Het
Zfyve28	T	C	5: 34,356,219 (GRCm39)	T761A	probably damaging	Het
Zswim8	G	A	14: 20,764,436 (GRCm39)	R602Q	probably damaging	Het

Other mutations in Spns2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01733:Spns2	APN	11	72,347,336 (GRCm39)	missense	possibly damaging	0.79
IGL01804:Spns2	APN	11	72,348,130 (GRCm39)	missense	possibly damaging	0.89
elderly	UTSW	11	72,347,196 (GRCm39)	critical splice acceptor site	probably null
homely	UTSW	11	72,347,686 (GRCm39)	missense	probably damaging	1.00
whistler	UTSW	11	72,349,513 (GRCm39)	nonsense	probably null
Wrinkled	UTSW	11	72,347,704 (GRCm39)	missense	possibly damaging	0.81
R0883:Spns2	UTSW	11	72,345,223 (GRCm39)	missense	probably damaging	1.00
R1544:Spns2	UTSW	11	72,347,193 (GRCm39)	missense	probably benign	0.30
R1696:Spns2	UTSW	11	72,347,173 (GRCm39)	missense	probably benign	0.25
R2046:Spns2	UTSW	11	72,349,866 (GRCm39)	missense	possibly damaging	0.49
R2164:Spns2	UTSW	11	72,349,497 (GRCm39)	missense	possibly damaging	0.82
R2259:Spns2	UTSW	11	72,348,094 (GRCm39)	missense	probably benign	0.35
R4209:Spns2	UTSW	11	72,345,012 (GRCm39)	missense	probably benign	0.07
R5285:Spns2	UTSW	11	72,380,305 (GRCm39)	missense	possibly damaging	0.92
R6883:Spns2	UTSW	11	72,347,196 (GRCm39)	critical splice acceptor site	probably null
R6990:Spns2	UTSW	11	72,380,447 (GRCm39)	missense	probably benign	0.08
R7221:Spns2	UTSW	11	72,347,742 (GRCm39)	missense	probably benign	0.43
R7227:Spns2	UTSW	11	72,349,513 (GRCm39)	nonsense	probably null
R7390:Spns2	UTSW	11	72,347,704 (GRCm39)	missense	possibly damaging	0.81
R7699:Spns2	UTSW	11	72,380,443 (GRCm39)	nonsense	probably null
R7700:Spns2	UTSW	11	72,380,443 (GRCm39)	nonsense	probably null
R8042:Spns2	UTSW	11	72,345,003 (GRCm39)	missense	possibly damaging	0.46
R8155:Spns2	UTSW	11	72,347,394 (GRCm39)	missense	possibly damaging	0.46
R8553:Spns2	UTSW	11	72,348,053 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CCAGTAAAGCAGGTAATGGCTCC -3'
(R):5'- GGCCTGAGAAAGCGCATTTC -3'

Sequencing Primer
(F):5'- TGGCTCCAAAGATGAGGCTGTG -3'
(R):5'- AAAGCGCATTTCTGTTTGGGGAAG -3'

Posted On

2019-06-26