Incidental Mutation 'R2404:Sgms1'
ID 248891
Institutional Source Beutler Lab
Gene Symbol Sgms1
Ensembl Gene ENSMUSG00000040451
Gene Name sphingomyelin synthase 1
Synonyms SMS1beta, SMS1gamma, SMS1alpha2, 9530058O11Rik, SMS1, Tmem23, SMS1alpha1
MMRRC Submission 040370-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.931) question?
Stock # R2404 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 32100127-32367114 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) G to A at 32137072 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Stop codon at position 165 (R165*)
Ref Sequence ENSEMBL: ENSMUSP00000119869 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000099514] [ENSMUST00000134415] [ENSMUST00000142618] [ENSMUST00000151289] [ENSMUST00000152340] [ENSMUST00000151822]
AlphaFold Q8VCQ6
Predicted Effect probably null
Transcript: ENSMUST00000099514
AA Change: R165*
SMART Domains Protein: ENSMUSP00000097114
Gene: ENSMUSG00000040451
AA Change: R165*

DomainStartEndE-ValueType
Pfam:SAM_1 11 74 1.3e-6 PFAM
transmembrane domain 141 163 N/A INTRINSIC
transmembrane domain 186 208 N/A INTRINSIC
Pfam:PAP2 216 362 4.5e-10 PFAM
Pfam:PAP2_C 282 355 4.9e-34 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124012
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131768
Predicted Effect probably null
Transcript: ENSMUST00000134415
AA Change: R165*
SMART Domains Protein: ENSMUSP00000115785
Gene: ENSMUSG00000040451
AA Change: R165*

DomainStartEndE-ValueType
Pfam:SAM_1 11 74 4.3e-7 PFAM
transmembrane domain 141 163 N/A INTRINSIC
transmembrane domain 188 210 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141655
Predicted Effect probably null
Transcript: ENSMUST00000142618
AA Change: R165*
SMART Domains Protein: ENSMUSP00000117336
Gene: ENSMUSG00000040451
AA Change: R165*

DomainStartEndE-ValueType
Pfam:SAM_1 11 74 1.3e-6 PFAM
transmembrane domain 141 163 N/A INTRINSIC
transmembrane domain 186 208 N/A INTRINSIC
Pfam:PAP2 216 362 4.5e-10 PFAM
Pfam:PAP2_C 282 355 4.9e-34 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000151289
AA Change: R165*
SMART Domains Protein: ENSMUSP00000123395
Gene: ENSMUSG00000040451
AA Change: R165*

DomainStartEndE-ValueType
Pfam:SAM_1 11 74 1.5e-6 PFAM
transmembrane domain 141 163 N/A INTRINSIC
transmembrane domain 186 208 N/A INTRINSIC
transmembrane domain 221 243 N/A INTRINSIC
Pfam:PAP2_C 282 355 1.7e-30 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000152340
AA Change: R165*
SMART Domains Protein: ENSMUSP00000119869
Gene: ENSMUSG00000040451
AA Change: R165*

DomainStartEndE-ValueType
Pfam:SAM_1 11 74 4.7e-7 PFAM
transmembrane domain 141 163 N/A INTRINSIC
transmembrane domain 188 210 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149107
Predicted Effect probably benign
Transcript: ENSMUST00000151822
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.2%
Validation Efficiency 98% (52/53)
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 predicted to be a five-pass transmembrane protein. This gene may be predominately expressed in brain. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit premature death, impaired insulin tolerance, increased insulin sensitivity, decreased insulin secretion, and abnormal pancreatic islet cell mitochondria morphology. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933402N03Rik T C 7: 130,740,923 (GRCm39) T98A possibly damaging Het
Aifm2 A G 10: 61,563,974 (GRCm39) I161V probably benign Het
Arhgef26 T C 3: 62,336,336 (GRCm39) M625T possibly damaging Het
Atp9a T A 2: 168,517,283 (GRCm39) probably null Het
Avpr1a T C 10: 122,285,115 (GRCm39) F136L possibly damaging Het
Bcas3 T C 11: 85,245,715 (GRCm39) probably benign Het
Bnc1 A T 7: 81,618,463 (GRCm39) H867Q probably benign Het
Cdh12 C T 15: 21,537,720 (GRCm39) T407I probably damaging Het
Chd5 C T 4: 152,451,791 (GRCm39) T701M probably damaging Het
Dhx57 A G 17: 80,561,733 (GRCm39) V927A probably damaging Het
Dnah2 A G 11: 69,328,047 (GRCm39) F3353L probably damaging Het
Ect2 G A 3: 27,185,999 (GRCm39) P495S probably benign Het
Egfl7 G A 2: 26,479,162 (GRCm39) E25K possibly damaging Het
Gm5117 T C 8: 32,227,306 (GRCm39) noncoding transcript Het
Hbs1l A T 10: 21,171,946 (GRCm39) probably benign Het
Insrr C T 3: 87,709,974 (GRCm39) T309I possibly damaging Het
Kalrn C T 16: 33,810,180 (GRCm39) D2525N possibly damaging Het
Kif12 A C 4: 63,088,790 (GRCm39) L170R probably damaging Het
Krt90 A G 15: 101,463,105 (GRCm39) probably null Het
Mcu A G 10: 59,303,526 (GRCm39) S104P probably damaging Het
Mical3 G A 6: 120,936,789 (GRCm39) P374S probably benign Het
Ncam2 A T 16: 81,287,128 (GRCm39) probably benign Het
Or12e9 A G 2: 87,202,568 (GRCm39) I231V probably benign Het
Or2t47 A T 11: 58,442,546 (GRCm39) I173N probably damaging Het
Or2w1b T C 13: 21,300,012 (GRCm39) L50P probably damaging Het
Or5k17 G A 16: 58,745,998 (GRCm39) S312L probably benign Het
Otud7a A G 7: 63,346,899 (GRCm39) S158G probably benign Het
Phlpp1 C T 1: 106,100,569 (GRCm39) T279M probably benign Het
Pkhd1l1 T G 15: 44,414,216 (GRCm39) W2828G probably damaging Het
Pnma8a A T 7: 16,694,316 (GRCm39) N57I probably damaging Het
Ppp4r4 A G 12: 103,547,749 (GRCm39) probably null Het
Ptprq T C 10: 107,522,460 (GRCm39) Y531C probably damaging Het
Rai1 A G 11: 60,080,750 (GRCm39) T1605A probably benign Het
Satb2 T C 1: 56,987,267 (GRCm39) Y106C probably damaging Het
Slc19a3 T A 1: 83,000,756 (GRCm39) H87L probably benign Het
Slc4a7 G T 14: 14,733,733 (GRCm38) V54L probably damaging Het
Sp110 A C 1: 85,505,050 (GRCm39) F434C probably benign Het
Spen T C 4: 141,205,216 (GRCm39) N1137S unknown Het
Spice1 T C 16: 44,186,989 (GRCm39) I162T probably benign Het
Spmip1 G A 6: 29,473,390 (GRCm39) R173Q probably benign Het
Sqor A T 2: 122,649,943 (GRCm39) T396S probably benign Het
Tshz3 A T 7: 36,469,805 (GRCm39) Q598L probably damaging Het
Ttc13 C T 8: 125,405,736 (GRCm39) probably benign Het
Ubxn2a T C 12: 4,933,851 (GRCm39) T187A probably benign Het
Usp28 T C 9: 48,948,558 (GRCm39) probably null Het
Zc3h12a T C 4: 125,013,316 (GRCm39) Y516C probably damaging Het
Zfp616 A C 11: 73,975,682 (GRCm39) K650N probably damaging Het
Other mutations in Sgms1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00486:Sgms1 APN 19 32,137,025 (GRCm39) missense probably damaging 1.00
IGL01585:Sgms1 APN 19 32,120,245 (GRCm39) missense probably damaging 1.00
IGL02490:Sgms1 APN 19 32,137,543 (GRCm39) missense probably damaging 0.98
IGL02970:Sgms1 APN 19 32,137,165 (GRCm39) missense probably damaging 0.99
R1051:Sgms1 UTSW 19 32,137,439 (GRCm39) missense probably damaging 1.00
R1871:Sgms1 UTSW 19 32,137,282 (GRCm39) missense probably benign 0.01
R1971:Sgms1 UTSW 19 32,137,357 (GRCm39) missense probably benign 0.05
R2001:Sgms1 UTSW 19 32,137,083 (GRCm39) missense possibly damaging 0.94
R2405:Sgms1 UTSW 19 32,137,072 (GRCm39) nonsense probably null
R2408:Sgms1 UTSW 19 32,137,072 (GRCm39) nonsense probably null
R2410:Sgms1 UTSW 19 32,137,072 (GRCm39) nonsense probably null
R3747:Sgms1 UTSW 19 32,136,994 (GRCm39) missense possibly damaging 0.65
R4016:Sgms1 UTSW 19 32,120,192 (GRCm39) missense possibly damaging 0.88
R4710:Sgms1 UTSW 19 32,137,537 (GRCm39) missense probably damaging 1.00
R5056:Sgms1 UTSW 19 32,137,087 (GRCm39) missense probably damaging 1.00
R5422:Sgms1 UTSW 19 32,137,232 (GRCm39) missense probably damaging 0.98
R6023:Sgms1 UTSW 19 32,101,773 (GRCm39) missense probably benign 0.12
R6106:Sgms1 UTSW 19 32,101,825 (GRCm39) missense possibly damaging 0.87
R6932:Sgms1 UTSW 19 32,120,193 (GRCm39) missense probably benign 0.02
R7207:Sgms1 UTSW 19 32,120,147 (GRCm39) missense probably null 1.00
R7382:Sgms1 UTSW 19 32,137,182 (GRCm39) missense possibly damaging 0.68
R7494:Sgms1 UTSW 19 32,107,091 (GRCm39) missense probably benign 0.00
R7712:Sgms1 UTSW 19 32,120,169 (GRCm39) missense probably benign 0.05
R7759:Sgms1 UTSW 19 32,137,276 (GRCm39) missense probably benign
R7872:Sgms1 UTSW 19 32,102,765 (GRCm39) missense probably damaging 0.99
R8283:Sgms1 UTSW 19 32,137,035 (GRCm39) missense probably damaging 1.00
R8377:Sgms1 UTSW 19 32,101,821 (GRCm39) missense probably damaging 1.00
R8487:Sgms1 UTSW 19 32,102,697 (GRCm39) missense probably benign 0.30
R8507:Sgms1 UTSW 19 32,137,109 (GRCm39) missense probably benign 0.06
R9007:Sgms1 UTSW 19 32,137,227 (GRCm39) missense probably benign 0.03
R9182:Sgms1 UTSW 19 32,101,758 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- CATGGCTGGATCTCAAGAGTG -3'
(R):5'- ATTGGCGTTGACATTCCCAAC -3'

Sequencing Primer
(F):5'- CATGGCTGGATCTCAAGAGTGTTTAC -3'
(R):5'- TGGCAGCTTCAGCATCAAG -3'
Posted On 2014-11-11