Mutagenetix > Incidental Mutation

Incidental Mutation 'R8816:Spns1'

672741

Institutional Source

Beutler Lab

Gene Symbol

Spns1

Ensembl Gene

ENSMUSG00000030741

Gene Name

SPNS lysolipid transporter 1, lysophospholipid

Synonyms

2210013K02Rik, spinster homolog

MMRRC Submission

068726-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8816 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

125969232-125976622 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 125971593 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Phenylalanine at position 319 (S319F)

Ref Sequence

ENSEMBL: ENSMUSP00000032994 (fasta)

Gene Model

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

AlphaFold

Q8R0G7

Predicted Effect

possibly damaging
Transcript: ENSMUST00000032994
AA Change: S319F

PolyPhen 2 Score 0.870 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000032994
Gene: ENSMUSG00000030741
AA Change: S319F

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

possibly damaging
Transcript: ENSMUST00000119754
AA Change: S319F

PolyPhen 2 Score 0.870 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000112555
Gene: ENSMUSG00000030741
AA Change: S319F

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 benign
Transcript: ENSMUST00000119846

SMART Domains

Protein: ENSMUSP00000112954
Gene: ENSMUSG00000030741

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

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

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

Predicted Effect

probably benign
Transcript: ENSMUST00000205366

Predicted Effect

probably benign
Transcript: ENSMUST00000205642

Predicted Effect

probably benign
Transcript: ENSMUST00000205930

Predicted Effect

probably benign
Transcript: ENSMUST00000206793

Meta Mutation Damage Score

0.1573

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca6	T	A	11: 110,127,513 (GRCm39)	H348L	probably benign	Het
Alpk1	A	T	3: 127,478,024 (GRCm39)	Y74*	probably null	Het
Ass1	T	C	2: 31,383,189 (GRCm39)		probably benign	Het
Atp8b4	C	T	2: 126,214,084 (GRCm39)		probably benign	Het
Atrn	C	A	2: 130,748,798 (GRCm39)	N106K	probably damaging	Het
Atrn	T	C	2: 130,846,494 (GRCm39)	V1256A	probably damaging	Het
Bicdl1	T	A	5: 115,862,804 (GRCm39)	Q150H	probably damaging	Het
Bltp3b	T	C	10: 89,626,597 (GRCm39)		probably benign	Het
Cdhr4	T	C	9: 107,872,791 (GRCm39)	V280A	possibly damaging	Het
Cfap54	C	T	10: 92,714,454 (GRCm39)	V2642I	unknown	Het
Chd2	T	C	7: 73,140,245 (GRCm39)	H661R	probably damaging	Het
Cntnap2	A	G	6: 46,833,076 (GRCm39)	D763G	possibly damaging	Het
Csnk1g2	T	C	10: 80,474,093 (GRCm39)	C160R	probably damaging	Het
Cyb5r4	T	C	9: 86,904,286 (GRCm39)	S19P	probably benign	Het
Cyp4a30b	G	A	4: 115,309,834 (GRCm39)	V12M	probably benign	Het
Dpp6	C	T	5: 27,930,711 (GRCm39)	P848S	probably benign	Het
Dzip1	T	C	14: 119,159,785 (GRCm39)	Y141C	probably benign	Het
Eif2b3	C	A	4: 116,928,052 (GRCm39)	Q424K	probably benign	Het
Fbxw14	G	A	9: 109,105,305 (GRCm39)	R287*	probably null	Het
Fcgbp	T	G	7: 27,784,412 (GRCm39)	S157R	probably benign	Het
Fmnl2	T	G	2: 53,004,214 (GRCm39)	V642G	unknown	Het
Gpr119	C	T	X: 47,762,276 (GRCm39)	R287Q	possibly damaging	Het
Grm7	C	T	6: 111,230,966 (GRCm39)	T463I	possibly damaging	Het
Haus4	G	A	14: 54,779,710 (GRCm39)	R305C	probably benign	Het
Htr1f	A	G	16: 64,746,537 (GRCm39)	S252P	probably benign	Het
Ino80b	T	C	6: 83,098,861 (GRCm39)	Q359R	probably damaging	Het
Itgad	C	A	7: 127,797,542 (GRCm39)	Y924*	probably null	Het
Itpr2	A	G	6: 146,142,710 (GRCm39)	Y1703H	probably damaging	Het
Kif5c	T	A	2: 49,584,799 (GRCm39)	V174E	probably damaging	Het
Kifc2	A	G	15: 76,548,371 (GRCm39)	E405G	probably damaging	Het
Klk1b3	T	C	7: 43,851,668 (GRCm39)	V242A	possibly damaging	Het
Kndc1	T	C	7: 139,517,909 (GRCm39)	F1615S	probably damaging	Het
Lmtk2	T	A	5: 144,112,793 (GRCm39)	L1171*	probably null	Het
Myh10	A	G	11: 68,693,778 (GRCm39)	E1530G	probably damaging	Het
Nav3	T	A	10: 109,699,721 (GRCm39)	S258C	possibly damaging	Het
Nudcd3	C	T	11: 6,100,587 (GRCm39)	G186S	probably damaging	Het
Or9s15	T	A	1: 92,524,768 (GRCm39)	C176S	probably damaging	Het
Otog	C	T	7: 45,950,905 (GRCm39)	S374F	possibly damaging	Het
P2ry2	T	A	7: 100,647,763 (GRCm39)	I181F	possibly damaging	Het
Pde11a	T	C	2: 76,121,577 (GRCm39)	I335V	probably benign	Het
Phyhip	A	C	14: 70,704,375 (GRCm39)	D198A	probably damaging	Het
Pik3r5	A	T	11: 68,385,060 (GRCm39)	Y655F	probably damaging	Het
Rab6a	T	C	7: 100,279,145 (GRCm39)	I95T	possibly damaging	Het
Sgsm1	T	C	5: 113,435,097 (GRCm39)	E99G	probably damaging	Het
Skint10	A	T	4: 112,603,892 (GRCm39)	F98L	probably benign	Het
Slc35c2	A	G	2: 165,119,378 (GRCm39)	S321P	probably benign	Het
Smyd1	T	A	6: 71,192,868 (GRCm39)	E447V	probably damaging	Het
Smyd4	T	C	11: 75,281,232 (GRCm39)	V235A	probably benign	Het
Sod2	A	G	17: 13,227,253 (GRCm39)	Y69C	probably benign	Het
Tfap2b	A	G	1: 19,284,337 (GRCm39)	S82G	probably benign	Het
Tln2	C	A	9: 67,128,693 (GRCm39)	E1465D	possibly damaging	Het
Tln2	A	G	9: 67,128,799 (GRCm39)	I1430T	probably damaging	Het
Trio	G	T	15: 27,741,357 (GRCm39)	N2680K	probably damaging	Het
Trmt10c	A	T	16: 55,854,522 (GRCm39)	V371D	probably damaging	Het
Trpm3	T	C	19: 22,965,580 (GRCm39)	S1692P	probably damaging	Het
Usb1	G	T	8: 96,071,984 (GRCm39)	C228F	probably benign	Het
Veph1	G	T	3: 66,065,646 (GRCm39)	H474N	probably benign	Het
Wls	A	G	3: 159,639,928 (GRCm39)	T520A	possibly damaging	Het
Ywhae	T	C	11: 75,623,878 (GRCm39)	Y9H	probably damaging	Het
Zranb3	C	T	1: 127,964,347 (GRCm39)	V127M	possibly 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
R4758:Spns1	UTSW	7	125,969,966 (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
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'- TGGGAGCTATTCCTTCTGCAAG -3'
(R):5'- GACTTCCTCTCAATGTCTGCAG -3'

Sequencing Primer
(F):5'- TCTGCAAGGTCCCCTGAC -3'
(R):5'- AATGTCTGCAGTCCTAGTTTCG -3'

Posted On

2021-04-30