Incidental Mutation 'R3552:Spns1'
ID 268996
Institutional Source Beutler Lab
Gene Symbol Spns1
Ensembl Gene ENSMUSG00000030741
Gene Name SPNS lysolipid transporter 1, lysophospholipid
Synonyms 2210013K02Rik, spinster homolog
MMRRC Submission 040669-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3552 (G1)
Quality Score 212
Status Validated
Chromosome 7
Chromosomal Location 125969232-125976622 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 125969543 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 512 (V512A)
Ref Sequence ENSEMBL: ENSMUSP00000032994 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032994] [ENSMUST00000032997] [ENSMUST00000119754] [ENSMUST00000119846] [ENSMUST00000205642] [ENSMUST00000206793] [ENSMUST00000205930] [ENSMUST00000205366] [ENSMUST00000138141] [ENSMUST00000150476]
AlphaFold Q8R0G7
Predicted Effect possibly damaging
Transcript: ENSMUST00000032994
AA Change: V512A

PolyPhen 2 Score 0.943 (Sensitivity: 0.80; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000032994
Gene: ENSMUSG00000030741
AA Change: V512A

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 possibly damaging
Transcript: ENSMUST00000119846
AA Change: V460A

PolyPhen 2 Score 0.495 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000112954
Gene: ENSMUSG00000030741
AA Change: V460A

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 probably benign
Transcript: ENSMUST00000205642
Predicted Effect probably benign
Transcript: ENSMUST00000206793
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205398
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150748
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206731
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184637
Predicted Effect probably benign
Transcript: ENSMUST00000205930
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152000
Predicted Effect probably benign
Transcript: ENSMUST00000205366
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206094
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
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
Meta Mutation Damage Score 0.0605 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 93.4%
Validation Efficiency 100% (66/66)
MGI Phenotype PHENOTYPE: Homozygous mutation results in lethality before weaning. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaca T A 11: 84,152,450 (GRCm39) Y866N probably damaging Het
Agk A G 6: 40,371,615 (GRCm39) T371A probably benign Het
Akna T C 4: 63,316,361 (GRCm39) M1V probably null Het
Aldh7a1 T C 18: 56,683,364 (GRCm39) probably null Het
Ankrd26 A T 6: 118,484,737 (GRCm39) L1500H probably damaging Het
Atp13a5 T A 16: 29,129,584 (GRCm39) D452V probably damaging Het
Bahcc1 C T 11: 120,167,598 (GRCm39) T1333M possibly damaging Het
Carmil3 G T 14: 55,744,859 (GRCm39) R1276L possibly damaging Het
Ccni T C 5: 93,335,620 (GRCm39) S173G probably benign Het
Chrm2 A T 6: 36,500,745 (GRCm39) I201F probably damaging Het
Col16a1 A G 4: 129,970,834 (GRCm39) T618A probably benign Het
Dele1 A G 18: 38,391,418 (GRCm39) probably benign Het
Dock2 T C 11: 34,611,787 (GRCm39) Y192C probably benign Het
Ep400 T A 5: 110,877,153 (GRCm39) E821V unknown Het
Esrrg G A 1: 187,882,387 (GRCm39) V215I probably benign Het
Evx1 A T 6: 52,293,908 (GRCm39) S359C probably damaging Het
Fcrl2 A G 3: 87,166,717 (GRCm39) I92T possibly damaging Het
Gal3st1 T A 11: 3,948,110 (GRCm39) F106I possibly damaging Het
Gm9944 T C 4: 144,179,613 (GRCm39) probably benign Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Hrc G C 7: 44,985,757 (GRCm39) E303Q possibly damaging Het
Kcnh1 A G 1: 191,921,074 (GRCm39) N118D probably damaging Het
Khdrbs1 A G 4: 129,614,584 (GRCm39) I323T possibly damaging Het
Klhdc7b T C 15: 89,271,724 (GRCm39) Y869H probably benign Het
Lrrc4c T A 2: 97,460,306 (GRCm39) W311R probably damaging Het
Megf11 A G 9: 64,602,745 (GRCm39) D862G possibly damaging Het
Muc5b A G 7: 141,415,072 (GRCm39) T2673A possibly damaging Het
Muc5b A G 7: 141,421,442 (GRCm39) S4311G probably benign Het
Myo15a C T 11: 60,400,489 (GRCm39) A1767V possibly damaging Het
Neo1 T A 9: 58,801,161 (GRCm39) K1140M probably damaging Het
Oc90 T C 15: 65,750,650 (GRCm39) Q365R possibly damaging Het
Oplah C T 15: 76,186,294 (GRCm39) D734N possibly damaging Het
Or1e19 T C 11: 73,316,678 (GRCm39) I44V probably benign Het
Or4c58 A C 2: 89,674,687 (GRCm39) M210R possibly damaging Het
Or9g3 T C 2: 85,590,237 (GRCm39) N161S possibly damaging Het
Pbx1 G A 1: 167,986,362 (GRCm39) P411L possibly damaging Het
Pcdhga6 G T 18: 37,841,270 (GRCm39) R330L probably benign Het
Phox2b C A 5: 67,254,999 (GRCm39) R150L probably damaging Het
Plscr2 A G 9: 92,172,848 (GRCm39) E169G probably damaging Het
Ptprn2 A T 12: 116,852,497 (GRCm39) Q518L probably benign Het
Rbl1 A T 2: 157,037,505 (GRCm39) I214K probably benign Het
Ryr1 T A 7: 28,756,422 (GRCm39) Q3464L probably damaging Het
Ryr3 T A 2: 112,582,132 (GRCm39) I2854F probably damaging Het
Shtn1 T C 19: 58,963,470 (GRCm39) Y615C probably benign Het
Sirt5 A T 13: 43,536,643 (GRCm39) N226Y probably damaging Het
Slc30a3 G A 5: 31,252,422 (GRCm39) probably benign Het
Slc5a4b A G 10: 75,917,358 (GRCm39) V226A probably damaging Het
Slf2 C A 19: 44,923,390 (GRCm39) S68* probably null Het
Smyd5 G A 6: 85,419,193 (GRCm39) E292K probably damaging Het
Sry T A Y: 2,663,141 (GRCm39) Q173L unknown Het
Ssrp1 C A 2: 84,874,736 (GRCm39) Q519K probably benign Het
Tgfbr3 T C 5: 107,287,705 (GRCm39) E498G probably damaging Het
Tnrc6b T G 15: 80,764,448 (GRCm39) L650W probably damaging Het
Tnxb A T 17: 34,937,695 (GRCm39) E3861D probably damaging Het
Trbc1 G T 6: 41,516,579 (GRCm39) probably benign Het
Trpm7 T A 2: 126,668,630 (GRCm39) probably benign Het
Usp39 G A 6: 72,314,815 (GRCm39) T197I possibly damaging Het
Vmn1r38 T C 6: 66,753,477 (GRCm39) H213R possibly damaging Het
Washc2 A G 6: 116,197,529 (GRCm39) D168G probably damaging Het
Washc4 A G 10: 83,382,720 (GRCm39) I45V probably benign Het
Zfp352 A G 4: 90,113,339 (GRCm39) E493G probably benign Het
Zfp692 C T 11: 58,200,254 (GRCm39) T170I possibly damaging Het
Zfp735 C A 11: 73,602,067 (GRCm39) S337* 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
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
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'- TCTGGGAGCTGGGAGATATC -3'
(R):5'- CTCATCCAGCTTAGCTTTGGG -3'

Sequencing Primer
(F):5'- GGAGATATCCCAGGGCTTCCTTC -3'
(R):5'- ATCCAGCTTAGCTTTGGGTCTGTC -3'
Posted On 2015-02-19