Incidental Mutation 'R8377:Sgms1'
ID 646786
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 067745-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.931) question?
Stock # R8377 (G1)
Quality Score 225.009
Status Not validated
Chromosome 19
Chromosomal Location 32100127-32367114 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 32101821 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 395 (Y395C)
Ref Sequence ENSEMBL: ENSMUSP00000097114 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000099514] [ENSMUST00000134415] [ENSMUST00000142618] [ENSMUST00000151289] [ENSMUST00000152340]
AlphaFold Q8VCQ6
PDB Structure Solution structure of the sam-domain of mouse phosphatidyl ceramidecholinephosphotransferase 1 [SOLUTION NMR]
Predicted Effect probably damaging
Transcript: ENSMUST00000099514
AA Change: Y395C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000097114
Gene: ENSMUSG00000040451
AA Change: Y395C

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 benign
Transcript: ENSMUST00000134415
SMART Domains Protein: ENSMUSP00000115785
Gene: ENSMUSG00000040451

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 probably damaging
Transcript: ENSMUST00000142618
AA Change: Y395C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000117336
Gene: ENSMUSG00000040451
AA Change: Y395C

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 damaging
Transcript: ENSMUST00000151289
AA Change: Y395C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000123395
Gene: ENSMUSG00000040451
AA Change: Y395C

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 benign
Transcript: ENSMUST00000152340
SMART Domains Protein: ENSMUSP00000119869
Gene: ENSMUSG00000040451

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acot3 C A 12: 84,105,561 (GRCm39) C251* probably null Het
Acsbg1 A G 9: 54,529,789 (GRCm39) C273R probably damaging Het
Adh6a A G 3: 138,031,884 (GRCm39) T259A probably damaging Het
Aknad1 A G 3: 108,689,255 (GRCm39) H639R possibly damaging Het
Alkal2 G T 12: 30,934,850 (GRCm39) G23V probably damaging Het
Ampd3 A G 7: 110,399,937 (GRCm39) R342G probably damaging Het
Arid5b G T 10: 67,933,217 (GRCm39) A895E probably damaging Het
BB014433 GCACACAGCTTTGGAGGTGTACACACCCGGGTTGGGGCCTCTACACACAGCTTTGGAGGTGTACACACCCGGGTTGGGGCCTCTGCACACAGCTTTGG GCACACAGCTTTGGAGGTGTACACACCCGGGTTGGGGCCTCTGCACACAGCTTTGG 8: 15,092,160 (GRCm39) probably benign Het
Bmp8a G T 4: 123,236,482 (GRCm39) P7Q unknown Het
Boll A C 1: 55,362,837 (GRCm39) V187G possibly damaging Het
Ccdc162 A T 10: 41,457,306 (GRCm39) C1544S probably benign Het
Cmss1 A C 16: 57,127,757 (GRCm39) M182R possibly damaging Het
Cntn3 T C 6: 102,186,254 (GRCm39) M578V probably benign Het
Dmxl2 A T 9: 54,286,032 (GRCm39) W2718R probably damaging Het
Dsg1a T A 18: 20,466,831 (GRCm39) I567N probably damaging Het
Epc2 T A 2: 49,412,527 (GRCm39) D168E probably damaging Het
Ern2 G A 7: 121,780,515 (GRCm39) Q162* probably null Het
F11r G T 1: 171,265,111 (GRCm39) probably benign Het
Fcgrt T C 7: 44,751,987 (GRCm39) Y59C probably damaging Het
Fmn2 G T 1: 174,436,011 (GRCm39) E661* probably null Het
Gbp4 T A 5: 105,266,328 (GRCm39) Q571L probably benign Het
Gm29106 A T 1: 118,126,593 (GRCm39) H95L probably damaging Het
Gphn G A 12: 78,711,280 (GRCm39) V621M probably damaging Het
Grwd1 T C 7: 45,480,036 (GRCm39) Y57C probably damaging Het
Insyn2b C A 11: 34,351,964 (GRCm39) A2D probably damaging Het
Irs2 G A 8: 11,054,848 (GRCm39) Q1195* probably null Het
Itpr1 G C 6: 108,487,699 (GRCm39) C2375S probably benign Het
Kcnmb4 A T 10: 116,282,290 (GRCm39) Y136N probably benign Het
Matn2 C T 15: 34,345,511 (GRCm39) P173S probably damaging Het
Med17 A C 9: 15,173,655 (GRCm39) D606E probably damaging Het
Mpl A G 4: 118,301,254 (GRCm39) V537A Het
Mrpl1 C G 5: 96,374,226 (GRCm39) A167G probably benign Het
Mrpl21 T C 19: 3,342,487 (GRCm39) F206S unknown Het
Msh6 T A 17: 88,292,598 (GRCm39) M451K probably damaging Het
Myo10 T C 15: 25,804,481 (GRCm39) I1592T possibly damaging Het
Naip1 A T 13: 100,562,374 (GRCm39) D930E possibly damaging Het
Necap2 T C 4: 140,795,534 (GRCm39) I242V probably benign Het
Nfya A G 17: 48,699,073 (GRCm39) V240A possibly damaging Het
Olfml2b A G 1: 170,496,353 (GRCm39) D328G probably damaging Het
Or10ak13 A T 4: 118,639,203 (GRCm39) M193K probably benign Het
Or4k35 T A 2: 111,099,983 (GRCm39) H243L probably damaging Het
Or5b24 T G 19: 12,912,399 (GRCm39) V99G probably benign Het
Or5p53 T G 7: 107,532,892 (GRCm39) L55R probably damaging Het
Phf8-ps C A 17: 33,286,038 (GRCm39) A255S probably benign Het
Pkd1l3 T C 8: 110,361,982 (GRCm39) V1018A probably benign Het
Plcg1 T C 2: 160,596,842 (GRCm39) L761P probably damaging Het
Ppp1r36 T C 12: 76,485,215 (GRCm39) S313P possibly damaging Het
Ptpru C A 4: 131,535,646 (GRCm39) G444C probably damaging Het
Rfxank A T 8: 70,587,960 (GRCm39) V149D probably damaging Het
Rimbp2 G A 5: 128,857,395 (GRCm39) H819Y probably damaging Het
Siae G A 9: 37,542,901 (GRCm39) probably null Het
Slc46a2 T A 4: 59,914,713 (GRCm39) D70V probably damaging Het
Smpdl3a A C 10: 57,677,032 (GRCm39) L43F possibly damaging Het
Spcs1 T A 14: 30,722,103 (GRCm39) D146V possibly damaging Het
Srcin1 T C 11: 97,442,804 (GRCm39) D8G probably damaging Het
Stra6 G T 9: 58,056,488 (GRCm39) L373F probably damaging Het
Tacc1 A T 8: 25,672,299 (GRCm39) S310T possibly damaging Het
Tlr12 T C 4: 128,509,566 (GRCm39) S895G probably benign Het
Tnfaip3 A G 10: 18,887,258 (GRCm39) V89A probably damaging Het
Top1 C T 2: 160,488,009 (GRCm39) probably benign Het
Trappc13 T G 13: 104,297,509 (GRCm39) I132L probably benign Het
Trpt1 C T 19: 6,976,349 (GRCm39) Q249* probably null Het
Tsnaxip1 A C 8: 106,569,179 (GRCm39) K510Q probably damaging Het
Usp39 A T 6: 72,305,657 (GRCm39) N375K probably benign Het
Vldlr T A 19: 27,212,258 (GRCm39) C91S probably damaging Het
Vmn1r232 T A 17: 21,134,239 (GRCm39) L120F probably benign Het
Vmn2r71 T C 7: 85,264,707 (GRCm39) V13A probably benign Het
Wdr11 T A 7: 129,208,412 (GRCm39) V389E possibly damaging Het
Wsb2 A T 5: 117,514,766 (GRCm39) I321F possibly damaging Het
Zan A T 5: 137,389,949 (GRCm39) V4841E unknown Het
Zfy1 A T Y: 725,723 (GRCm39) F681I possibly damaging Het
Zpld1 C A 16: 55,067,017 (GRCm39) E179D probably benign 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
R2404:Sgms1 UTSW 19 32,137,072 (GRCm39) nonsense probably null
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
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'- ACAGTGCTGAGCAGGTAAC -3'
(R):5'- GAGCAAGTCTGGGATCCTTTG -3'

Sequencing Primer
(F):5'- CAGGTAACGCAATAGGTTAAGTC -3'
(R):5'- CTGGGATCCTTTGAATTTTAACATGG -3'
Posted On 2020-09-02