Mutagenetix > Incidental Mutation

Incidental Mutation 'R4758:Spns1'

358325

Institutional Source

Beutler Lab

Gene Symbol

Spns1

Ensembl Gene

ENSMUSG00000030741

Gene Name

SPNS lysolipid transporter 1, lysophospholipid

Synonyms

2210013K02Rik, spinster homolog

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4758 (G1)

Quality Score

206

Status

Not validated

Chromosome

Chromosomal Location

125969232-125976622 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 125969966 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Tyrosine at position 478 (F478Y)

Ref Sequence

ENSEMBL: ENSMUSP00000032994 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032994] [ENSMUST00000032997] [ENSMUST00000119754] [ENSMUST00000119846] [ENSMUST00000138141] [ENSMUST00000205930] [ENSMUST00000205366] [ENSMUST00000206793] [ENSMUST00000205642] [ENSMUST00000150476]

AlphaFold

Q8R0G7

Predicted Effect

probably damaging
Transcript: ENSMUST00000032994
AA Change: F478Y

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

SMART Domains

Protein: ENSMUSP00000032994
Gene: ENSMUSG00000030741
AA Change: F478Y

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
Pfam:Sugar_tr	60	250	4.6e-15	PFAM
Pfam:OATP	60	385	1.5e-9	PFAM
Pfam:MFS_1	65	435	1.8e-34	PFAM
transmembrane domain	462	484	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000032997

SMART Domains

Protein: ENSMUSP00000032997
Gene: ENSMUSG00000030742

Domain	Start	End	E-Value	Type
Pfam:LAT	1	242	4.3e-121	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000119754

SMART Domains

Protein: ENSMUSP00000112555
Gene: ENSMUSG00000030741

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
Pfam:OATP	58	147	1.2e-8	PFAM
Pfam:Sugar_tr	60	250	1.3e-14	PFAM
Pfam:MFS_1	65	430	2.4e-34	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000119846
AA Change: F426Y

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000112954
Gene: ENSMUSG00000030741
AA Change: F426Y

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
Pfam:OATP	58	147	1.4e-8	PFAM
Pfam:Sugar_tr	60	250	1.5e-14	PFAM
Pfam:MFS_1	65	433	2.5e-26	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126810

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137263

Predicted Effect

probably benign
Transcript: ENSMUST00000138141

SMART Domains

Protein: ENSMUSP00000117803
Gene: ENSMUSG00000030741

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
Pfam:OATP	58	151	1.4e-9	PFAM
Pfam:MFS_1	65	149	1.5e-11	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000205930
AA Change: F243Y

PolyPhen 2 Score 0.518 (Sensitivity: 0.88; Specificity: 0.90)

Predicted Effect

probably benign
Transcript: ENSMUST00000205366

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150748

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152000

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206731

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205398

Predicted Effect

probably benign
Transcript: ENSMUST00000206793

Predicted Effect

probably benign
Transcript: ENSMUST00000205642

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184637

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206094

Predicted Effect

probably benign
Transcript: ENSMUST00000150476

SMART Domains

Protein: ENSMUSP00000115152
Gene: ENSMUSG00000030741

Domain	Start	End	E-Value	Type
Pfam:OATP	28	120	1.3e-8	PFAM
Pfam:Sugar_tr	28	220	1.6e-15	PFAM
Pfam:MFS_1	35	237	2.4e-31	PFAM

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.8%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Homozygous mutation results in lethality before weaning. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad9	T	A	3: 36,127,754 (GRCm39)	Y119N	probably damaging	Het
Actn2	T	A	13: 12,303,472 (GRCm39)	K443*	probably null	Het
Adgrb2	A	G	4: 129,903,143 (GRCm39)	N581S	probably damaging	Het
Afg2a	T	A	3: 37,487,385 (GRCm39)	S416T	probably benign	Het
Alb	A	T	5: 90,616,452 (GRCm39)	H319L	probably benign	Het
Aox1	A	G	1: 58,371,741 (GRCm39)	I802V	probably benign	Het
Arhgap45	G	A	10: 79,866,127 (GRCm39)	G995E	probably benign	Het
Capn12	A	C	7: 28,592,148 (GRCm39)	T689P	possibly damaging	Het
Cars1	T	C	7: 143,125,304 (GRCm39)	S312G	probably benign	Het
Cast	T	A	13: 74,887,999 (GRCm39)	D216V	possibly damaging	Het
Ccdc13	C	T	9: 121,662,800 (GRCm39)	E72K	possibly damaging	Het
Cd300lg	G	T	11: 101,944,417 (GRCm39)		probably null	Het
Cep41	A	G	6: 30,671,368 (GRCm39)		probably benign	Het
Chrna3	A	G	9: 54,929,560 (GRCm39)	Y93H	probably damaging	Het
Cic	A	G	7: 24,991,636 (GRCm39)	R1309G	possibly damaging	Het
Clcnkb	A	G	4: 141,135,160 (GRCm39)	V526A	probably benign	Het
Clec4a1	G	T	6: 122,910,825 (GRCm39)	V227F	probably damaging	Het
Cpa5	C	A	6: 30,615,159 (GRCm39)	H99N	possibly damaging	Het
Crem	C	A	18: 3,327,527 (GRCm39)	C4F	probably damaging	Het
Cybb	C	G	X: 9,316,989 (GRCm39)	D246H	probably benign	Het
Decr2	C	A	17: 26,307,914 (GRCm39)	E46D	probably damaging	Het
Dlg1	G	A	16: 31,610,570 (GRCm39)	V284I	possibly damaging	Het
Dnah3	T	C	7: 119,678,629 (GRCm39)	E360G	probably benign	Het
Dnajc1	A	T	2: 18,313,757 (GRCm39)	Y121*	probably null	Het
Dnajc13	A	G	9: 104,049,773 (GRCm39)	F1783L	probably damaging	Het
Eps8l2	T	A	7: 140,940,286 (GRCm39)	D505E	probably damaging	Het
Eral1	G	A	11: 77,966,425 (GRCm39)	T251I	probably benign	Het
Eya3	T	C	4: 132,422,196 (GRCm39)		probably null	Het
Fam120a	G	A	13: 49,034,333 (GRCm39)	T1093I	probably benign	Het
Fbn2	C	T	18: 58,159,458 (GRCm39)	A2424T	probably benign	Het
Git2	G	A	5: 114,868,412 (GRCm39)	T256M	probably damaging	Het
Gm9805	A	T	17: 22,689,871 (GRCm38)	Y34F	probably benign	Het
Itgb7	T	G	15: 102,124,642 (GRCm39)	T792P	probably benign	Het
Jakmip1	T	A	5: 37,285,966 (GRCm39)	I665N	probably damaging	Het
Kcnt2	T	C	1: 140,446,635 (GRCm39)	Y677H	probably damaging	Het
Klhdc4	G	A	8: 122,524,783 (GRCm39)	P382S	probably benign	Het
Knl1	TCC	TC	2: 118,902,213 (GRCm39)		probably null	Het
Lamb3	T	A	1: 193,022,269 (GRCm39)	M1039K	possibly damaging	Het
Lipm	A	T	19: 34,078,570 (GRCm39)	M1L	possibly damaging	Het
Lrrc37	A	G	11: 103,505,290 (GRCm39)	V2226A	possibly damaging	Het
Magi3	T	A	3: 103,922,637 (GRCm39)	D1360V	probably benign	Het
Mier2	C	A	10: 79,386,182 (GRCm39)	C23F	probably damaging	Het
Myo1h	C	T	5: 114,487,643 (GRCm39)	R616C	probably damaging	Het
Nars2	A	G	7: 96,622,735 (GRCm39)	D187G	probably damaging	Het
Nbea	T	C	3: 55,912,824 (GRCm39)	M988V	probably benign	Het
Nlrc5	C	A	8: 95,238,956 (GRCm39)	Q1465K	possibly damaging	Het
Nlrp4e	T	C	7: 23,020,043 (GRCm39)	F177L	probably benign	Het
Oas1a	A	G	5: 121,045,401 (GRCm39)	F47L	probably damaging	Het
Oas1f	A	G	5: 120,985,545 (GRCm39)	E30G	probably damaging	Het
Obscn	A	T	11: 58,894,189 (GRCm39)	M6689K	unknown	Het
Obscn	A	T	11: 59,026,743 (GRCm39)	D153E	probably damaging	Het
Or52s6	A	C	7: 103,092,076 (GRCm39)	C85G	probably damaging	Het
Osmr	A	T	15: 6,882,036 (GRCm39)	I36K	probably benign	Het
Pcf11	A	T	7: 92,310,383 (GRCm39)	F535Y	probably damaging	Het
Pde2a	C	T	7: 101,160,706 (GRCm39)	R886C	probably damaging	Het
Pik3ca	T	A	3: 32,492,127 (GRCm39)	C242S	probably benign	Het
Pikfyve	T	A	1: 65,311,674 (GRCm39)	D1925E	possibly damaging	Het
Plekhm2	A	T	4: 141,369,316 (GRCm39)	Y123N	possibly damaging	Het
Pomt2	A	T	12: 87,169,652 (GRCm39)	V406D	probably damaging	Het
Ppfia2	G	C	10: 106,597,978 (GRCm39)	L180F	probably damaging	Het
Prdm10	A	T	9: 31,273,708 (GRCm39)	T985S	probably benign	Het
Proc	T	A	18: 32,256,863 (GRCm39)	Y268F	probably damaging	Het
Prrc1	C	T	18: 57,517,320 (GRCm39)	T365M	probably damaging	Het
Rasa1	A	T	13: 85,382,567 (GRCm39)	D446E	probably benign	Het
Ribc2	T	A	15: 85,025,867 (GRCm39)	L281Q	probably damaging	Het
Runx1t1	A	G	4: 13,865,907 (GRCm39)	D385G	probably damaging	Het
Sdk2	A	G	11: 113,717,880 (GRCm39)	S1495P	possibly damaging	Het
Slc15a3	G	T	19: 10,831,726 (GRCm39)		probably null	Het
Slc43a3	A	G	2: 84,774,869 (GRCm39)	N149S	probably damaging	Het
Specc1l	A	G	10: 75,082,182 (GRCm39)	Q543R	probably damaging	Het
Spef1	T	C	2: 131,014,661 (GRCm39)		probably null	Het
Srebf2	T	C	15: 82,080,370 (GRCm39)	V821A	probably benign	Het
Stac3	A	G	10: 127,339,214 (GRCm39)	M108V	possibly damaging	Het
Stradb	A	G	1: 59,027,730 (GRCm39)	T87A	probably benign	Het
Stxbp5l	A	T	16: 36,954,592 (GRCm39)	M906K	probably benign	Het
Tex14	T	C	11: 87,405,311 (GRCm39)	V741A	probably benign	Het
Thoc2l	A	C	5: 104,668,265 (GRCm39)	E929A	possibly damaging	Het
Tpo	C	A	12: 30,125,870 (GRCm39)	G830C	probably damaging	Het
Unc79	T	A	12: 103,128,080 (GRCm39)	C2308*	probably null	Het
Vmn1r205	T	C	13: 22,777,016 (GRCm39)	T29A	possibly damaging	Het
Vmn1r69	G	A	7: 10,314,473 (GRCm39)	T7I	probably benign	Het
Vmn2r27	T	G	6: 124,208,596 (GRCm39)	T50P	possibly damaging	Het
Wdr83	A	G	8: 85,801,867 (GRCm39)	Y302H	probably benign	Het
Xirp2	A	T	2: 67,346,879 (GRCm39)	E3040V	probably damaging	Het
Zfp629	C	A	7: 127,209,758 (GRCm39)	G684W	probably damaging	Het

Other mutations in Spns1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00848:Spns1	APN	7	125,970,414 (GRCm39)	splice site	probably null
IGL02353:Spns1	APN	7	125,974,312 (GRCm39)	missense	probably damaging	1.00
IGL02561:Spns1	APN	7	125,972,941 (GRCm39)	critical splice donor site	probably null
IGL03403:Spns1	APN	7	125,970,708 (GRCm39)	splice site	probably null
R1634:Spns1	UTSW	7	125,970,343 (GRCm39)	unclassified	probably benign
R2327:Spns1	UTSW	7	125,969,958 (GRCm39)	missense	probably damaging	1.00
R3552:Spns1	UTSW	7	125,969,543 (GRCm39)	missense	possibly damaging	0.94
R3916:Spns1	UTSW	7	125,970,711 (GRCm39)	critical splice donor site	probably null
R4025:Spns1	UTSW	7	125,976,118 (GRCm39)	nonsense	probably null
R4095:Spns1	UTSW	7	125,969,958 (GRCm39)	missense	probably damaging	1.00
R4656:Spns1	UTSW	7	125,973,474 (GRCm39)	unclassified	probably benign
R4657:Spns1	UTSW	7	125,973,474 (GRCm39)	unclassified	probably benign
R4697:Spns1	UTSW	7	125,976,209 (GRCm39)	missense	probably damaging	1.00
R5062:Spns1	UTSW	7	125,973,501 (GRCm39)	unclassified	probably benign
R5371:Spns1	UTSW	7	125,972,936 (GRCm39)	unclassified	probably benign
R5700:Spns1	UTSW	7	125,971,641 (GRCm39)	missense	possibly damaging	0.95
R5973:Spns1	UTSW	7	125,969,495 (GRCm39)	missense	probably damaging	1.00
R5985:Spns1	UTSW	7	125,975,902 (GRCm39)	missense	probably benign	0.37
R6660:Spns1	UTSW	7	125,974,237 (GRCm39)	critical splice donor site	probably null
R7175:Spns1	UTSW	7	125,972,961 (GRCm39)	missense	probably damaging	0.98
R7937:Spns1	UTSW	7	125,973,226 (GRCm39)	missense	probably damaging	0.99
R8051:Spns1	UTSW	7	125,971,708 (GRCm39)	missense	probably benign	0.37
R8815:Spns1	UTSW	7	125,971,593 (GRCm39)	missense	possibly damaging	0.87
R8816:Spns1	UTSW	7	125,971,593 (GRCm39)	missense	possibly damaging	0.87
R8835:Spns1	UTSW	7	125,971,593 (GRCm39)	missense	possibly damaging	0.87
R8836:Spns1	UTSW	7	125,971,593 (GRCm39)	missense	possibly damaging	0.87
R8837:Spns1	UTSW	7	125,971,593 (GRCm39)	missense	possibly damaging	0.87
R9311:Spns1	UTSW	7	125,972,995 (GRCm39)	missense	probably damaging	1.00
Z1177:Spns1	UTSW	7	125,971,583 (GRCm39)	critical splice donor site	probably null
Z1177:Spns1	UTSW	7	125,971,582 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- GCATGAATGGATGGGCTAGTC -3'
(R):5'- AGGAAGGTTTTGCCCGTTAG -3'

Sequencing Primer
(F):5'- CTAGTCTGAGTGGAGGGAGAACTG -3'
(R):5'- TAGGCTGTGGGTCTCACC -3'

Posted On

2015-11-11