Incidental Mutation 'R4095:Spns1'
ID 317857
Institutional Source Beutler Lab
Gene Symbol Spns1
Ensembl Gene ENSMUSG00000030741
Gene Name SPNS lysolipid transporter 1, lysophospholipid
Synonyms 2210013K02Rik, spinster homolog
MMRRC Submission 040858-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4095 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 125969232-125976622 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 125969958 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 481 (T481A)
Ref Sequence ENSEMBL: ENSMUSP00000032994 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032994] [ENSMUST00000032997] [ENSMUST00000119754] [ENSMUST00000119846] [ENSMUST00000205930] [ENSMUST00000205366] [ENSMUST00000206793] [ENSMUST00000205642] [ENSMUST00000150476] [ENSMUST00000138141]
AlphaFold Q8R0G7
Predicted Effect probably damaging
Transcript: ENSMUST00000032994
AA Change: T481A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000032994
Gene: ENSMUSG00000030741
AA Change: T481A

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:LAT 1 242 4.3e-121 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000119754
SMART Domains Protein: ENSMUSP00000112555
Gene: ENSMUSG00000030741

DomainStartEndE-ValueType
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
AA Change: T429A

PolyPhen 2 Score 0.299 (Sensitivity: 0.91; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000112954
Gene: ENSMUSG00000030741
AA Change: T429A

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000205930
AA Change: T246A

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150748
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205398
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152000
Predicted Effect probably benign
Transcript: ENSMUST00000205366
Predicted Effect probably benign
Transcript: ENSMUST00000206793
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206094
Predicted Effect probably benign
Transcript: ENSMUST00000205642
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184637
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206731
Predicted Effect probably benign
Transcript: ENSMUST00000150476
SMART Domains Protein: ENSMUSP00000115152
Gene: ENSMUSG00000030741

DomainStartEndE-ValueType
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: ENSMUST00000138141
SMART Domains Protein: ENSMUSP00000117803
Gene: ENSMUSG00000030741

DomainStartEndE-ValueType
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
Meta Mutation Damage Score 0.1192 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.8%
Validation Efficiency 97% (59/61)
MGI Phenotype PHENOTYPE: Homozygous mutation results in lethality before weaning. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akap6 A T 12: 53,186,245 (GRCm39) I1220L probably damaging Het
Alas1 G T 9: 106,119,000 (GRCm39) probably null Het
Apba1 A T 19: 23,921,388 (GRCm39) Q737L probably benign Het
Arvcf T A 16: 18,220,327 (GRCm39) D564E probably damaging Het
Bcl11b G T 12: 107,883,094 (GRCm39) P335Q probably damaging Het
Brd9 G A 13: 74,092,918 (GRCm39) V302I probably benign Het
Brinp3 C A 1: 146,777,430 (GRCm39) H626N possibly damaging Het
C1qc T C 4: 136,617,637 (GRCm39) N153S probably benign Het
Casp3 G A 8: 47,087,251 (GRCm39) G66D probably damaging Het
Coq7 T G 7: 118,126,701 (GRCm39) probably null Het
Dach1 C T 14: 98,138,815 (GRCm39) V491M possibly damaging Het
Dda1 A G 8: 71,926,436 (GRCm39) T52A possibly damaging Het
Entpd7 A G 19: 43,692,640 (GRCm39) Y65C probably damaging Het
Fmnl2 A G 2: 52,991,535 (GRCm39) D350G probably damaging Het
Foxn3 G T 12: 99,162,700 (GRCm39) D400E probably damaging Het
Gbp2 A G 3: 142,343,210 (GRCm39) T576A probably benign Het
Gm15446 T A 5: 110,088,590 (GRCm39) probably null Het
Gtf2a1 G T 12: 91,542,411 (GRCm39) T57K possibly damaging Het
Hps5 T C 7: 46,425,218 (GRCm39) E494G probably benign Het
Htr2a G A 14: 74,943,789 (GRCm39) M456I probably benign Het
Hydin A G 8: 111,268,179 (GRCm39) N2886S probably damaging Het
Ighv2-6-8 T C 12: 113,759,773 (GRCm39) Y112C probably damaging Het
Kcnf1 A T 12: 17,225,480 (GRCm39) L247Q possibly damaging Het
Kndc1 A G 7: 139,516,938 (GRCm39) M1606V possibly damaging Het
Krt27 T C 11: 99,236,619 (GRCm39) T431A probably benign Het
Lama4 A T 10: 38,973,118 (GRCm39) I1562F probably damaging Het
Lrig1 T C 6: 94,590,559 (GRCm39) D487G probably benign Het
Lrp1b G A 2: 41,339,203 (GRCm39) T880I probably benign Het
Ltbp4 A G 7: 27,024,641 (GRCm39) V663A possibly damaging Het
Mapt T C 11: 104,201,362 (GRCm39) probably null Het
Mpdz A T 4: 81,302,060 (GRCm39) V229D possibly damaging Het
Or10am5 T A 7: 6,518,252 (GRCm39) S59C possibly damaging Het
Or6e1 T C 14: 54,520,188 (GRCm39) T55A probably benign Het
Or8s10 T C 15: 98,335,563 (GRCm39) L71P probably damaging Het
Parm1 T C 5: 91,742,039 (GRCm39) S136P probably benign Het
Pcdhgb2 T A 18: 37,824,003 (GRCm39) S331R probably benign Het
Pdxk T C 10: 78,300,644 (GRCm39) H13R probably damaging Het
Ppp1r12c T C 7: 4,486,366 (GRCm39) E601G probably damaging Het
Rell1 C A 5: 64,126,013 (GRCm39) V22L probably benign Het
Sema6c T A 3: 95,080,505 (GRCm39) L901Q probably benign Het
Sfswap A G 5: 129,637,805 (GRCm39) S821G possibly damaging Het
Slc22a23 A G 13: 34,489,189 (GRCm39) L116P probably damaging Het
Slit1 A T 19: 41,596,925 (GRCm39) probably benign Het
Tmem104 T A 11: 115,134,749 (GRCm39) Y427* probably null Het
Tmem74 G A 15: 43,730,678 (GRCm39) Q122* probably null Het
Tnpo2 T A 8: 85,765,048 (GRCm39) L10Q probably damaging Het
Trav6-2 G T 14: 52,905,272 (GRCm39) A98S probably benign Het
Ttll5 A T 12: 86,003,376 (GRCm39) R214* probably null Het
Ube2b A C 11: 51,888,654 (GRCm39) V39G possibly damaging Het
Vmn1r185 A T 7: 26,311,208 (GRCm39) V99E probably damaging Het
Wnk1 G A 6: 119,925,087 (GRCm39) T1459I probably damaging Het
Zc3h7a T C 16: 10,963,099 (GRCm39) K754R probably damaging Het
Zfp605 A G 5: 110,275,602 (GRCm39) K240R probably damaging Het
Zfp61 A G 7: 23,990,700 (GRCm39) probably null Het
Other mutations in Spns1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- CAGACCCAAAGCTAAGCTGG -3'
(R):5'- GCCATAGGAAGGTTTTGCCC -3'

Sequencing Primer
(F):5'- ATGCTGGGACTCTTGCCC -3'
(R):5'- CCATAGGAAGGTTTTGCCCGTTAG -3'
Posted On 2015-05-15