Mutagenetix > Incidental Mutation

Incidental Mutation 'R1971:Sgms1'

221000

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

039984-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.931) question?

Stock #

R1971 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

32100127-32367114 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 32137357 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Leucine at position 70 (I70L)

Ref Sequence

ENSEMBL: ENSMUSP00000115785 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000099514] [ENSMUST00000134415] [ENSMUST00000142618] [ENSMUST00000151289] [ENSMUST00000152340] [ENSMUST00000151822]

AlphaFold

Q8VCQ6

Predicted Effect

probably benign
Transcript: ENSMUST00000099514
AA Change: I70L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000097114
Gene: ENSMUSG00000040451
AA Change: I70L

Domain	Start	End	E-Value	Type
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 benign
Transcript: ENSMUST00000134415
AA Change: I70L

PolyPhen 2 Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000115785
Gene: ENSMUSG00000040451
AA Change: I70L

Domain	Start	End	E-Value	Type
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 benign
Transcript: ENSMUST00000142618
AA Change: I70L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000117336
Gene: ENSMUSG00000040451
AA Change: I70L

Domain	Start	End	E-Value	Type
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: ENSMUST00000149107

Predicted Effect

probably benign
Transcript: ENSMUST00000151289
AA Change: I70L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000123395
Gene: ENSMUSG00000040451
AA Change: I70L

Domain	Start	End	E-Value	Type
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
AA Change: I70L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000119869
Gene: ENSMUSG00000040451
AA Change: I70L

Domain	Start	End	E-Value	Type
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

probably benign
Transcript: ENSMUST00000151822

Meta Mutation Damage Score

0.0743

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.3%

Validation Efficiency

99% (115/116)

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001O22Rik	A	T	2: 30,686,566 (GRCm39)	I242N	probably benign	Het
2510009E07Rik	G	T	16: 21,472,048 (GRCm39)	Y217*	probably null	Het
4931429L15Rik	C	T	9: 46,220,086 (GRCm39)	V149M	probably benign	Het
Abcg8	G	T	17: 85,002,587 (GRCm39)		probably benign	Het
Acox1	A	G	11: 116,089,087 (GRCm39)	F77S	probably benign	Het
Adgrb3	G	T	1: 25,586,525 (GRCm39)	H389Q	probably benign	Het
Ak7	A	G	12: 105,692,504 (GRCm39)	N186S	probably damaging	Het
Apobr	A	G	7: 126,185,397 (GRCm39)	T303A	probably benign	Het
Arnt	C	T	3: 95,355,704 (GRCm39)	S16L	possibly damaging	Het
Bcl9l	T	C	9: 44,419,996 (GRCm39)		probably null	Het
Bco2	T	C	9: 50,457,284 (GRCm39)	D86G	probably damaging	Het
Bmpr1b	T	A	3: 141,563,333 (GRCm39)	I204F	probably damaging	Het
Bpifb5	C	A	2: 154,072,264 (GRCm39)	Q324K	probably benign	Het
Cacna2d2	G	A	9: 107,389,205 (GRCm39)	V223I	probably damaging	Het
Capn3	A	G	2: 120,311,228 (GRCm39)	D105G	possibly damaging	Het
Ccdc40	G	T	11: 119,153,901 (GRCm39)		probably null	Het
Ccdc83	T	A	7: 89,893,362 (GRCm39)	S132C	probably damaging	Het
Ckap2l	A	G	2: 129,127,342 (GRCm39)	S279P	possibly damaging	Het
Cldn12	C	A	5: 5,558,137 (GRCm39)	A97S	probably benign	Het
Clec2l	T	G	6: 38,640,309 (GRCm39)	S47A	probably benign	Het
Csnk1d	C	A	11: 120,863,274 (GRCm39)	R222M	possibly damaging	Het
Ctnna1	T	A	18: 35,287,580 (GRCm39)	D96E	probably benign	Het
D630045J12Rik	T	C	6: 38,145,078 (GRCm39)	D1316G	probably damaging	Het
Ddx4	C	T	13: 112,736,547 (GRCm39)	V608I	probably damaging	Het
Dmtf1	T	C	5: 9,198,989 (GRCm39)	E48G	probably benign	Het
Dnah17	G	C	11: 117,995,361 (GRCm39)	Q996E	probably benign	Het
Dnah9	G	C	11: 65,739,197 (GRCm39)	N4180K	probably damaging	Het
Dpf3	T	A	12: 83,371,809 (GRCm39)		probably null	Het
Drd2	T	C	9: 49,318,359 (GRCm39)	F434L	probably damaging	Het
En1	A	G	1: 120,534,742 (GRCm39)	T344A	unknown	Het
Eri3	A	G	4: 117,421,964 (GRCm39)	T81A	probably benign	Het
Fam20a	T	C	11: 109,576,237 (GRCm39)	Y174C	probably damaging	Het
Fam234a	G	C	17: 26,435,629 (GRCm39)		probably null	Het
Fam76a	A	T	4: 132,631,294 (GRCm39)	I217N	probably damaging	Het
Fancm	T	A	12: 65,148,466 (GRCm39)	S694T	probably benign	Het
Fcgbpl1	C	A	7: 27,830,937 (GRCm39)	A50E	possibly damaging	Het
Foxo3	A	G	10: 42,073,258 (GRCm39)	S420P	probably benign	Het
Foxp4	C	T	17: 48,186,796 (GRCm39)	R378Q	unknown	Het
Gm136	T	G	4: 34,755,986 (GRCm39)	D9A	probably benign	Het
Gstt2	G	T	10: 75,668,499 (GRCm39)	T116N	probably benign	Het
Hs3st6	A	G	17: 24,972,267 (GRCm39)	T70A	probably benign	Het
Hspa14	A	G	2: 3,490,804 (GRCm39)	V461A	possibly damaging	Het
Itih5	A	T	2: 10,243,379 (GRCm39)	D372V	probably damaging	Het
Kcna2	A	T	3: 107,012,140 (GRCm39)	R240S	probably damaging	Het
Kctd18	T	C	1: 58,006,779 (GRCm39)	I24V	probably benign	Het
Lap3	T	C	5: 45,663,508 (GRCm39)		probably benign	Het
Lcp1	T	C	14: 75,437,946 (GRCm39)	S119P	probably damaging	Het
Lig3	G	C	11: 82,686,544 (GRCm39)	D642H	probably benign	Het
Lpin1	A	T	12: 16,630,724 (GRCm39)	L58H	probably damaging	Het
Map4k5	G	T	12: 69,873,102 (GRCm39)	P468Q	possibly damaging	Het
Med31	G	A	11: 72,106,244 (GRCm39)		probably benign	Het
Mki67	A	T	7: 135,315,688 (GRCm39)		probably null	Het
Mrc1	G	A	2: 14,249,103 (GRCm39)		probably null	Het
Msh3	A	G	13: 92,359,784 (GRCm39)	I16T	probably damaging	Het
Msh3	T	A	13: 92,386,328 (GRCm39)		probably benign	Het
Mst1r	A	T	9: 107,790,411 (GRCm39)	I675F	probably benign	Het
Myb	A	C	10: 21,016,555 (GRCm39)	S652A	probably benign	Het
Myh2	G	T	11: 67,080,004 (GRCm39)	S1099I	possibly damaging	Het
Myl6b	A	G	10: 128,330,512 (GRCm39)	V181A	probably damaging	Het
Myt1l	A	T	12: 29,877,091 (GRCm39)	K247N	unknown	Het
Nanos2	G	T	7: 18,721,629 (GRCm39)	V34L	probably benign	Het
Nav1	T	C	1: 135,460,091 (GRCm39)	T411A	probably benign	Het
Nedd9	T	A	13: 41,492,424 (GRCm39)	I23F	probably damaging	Het
Nes	G	A	3: 87,885,634 (GRCm39)	V1254I	possibly damaging	Het
Nol6	A	G	4: 41,119,542 (GRCm39)	F588S	probably damaging	Het
Numa1	C	T	7: 101,658,529 (GRCm39)	A1605V	probably damaging	Het
Ofd1	T	C	X: 165,210,210 (GRCm39)	Y205C	probably benign	Het
Olr1	T	C	6: 129,470,498 (GRCm39)	E223G	probably benign	Het
Or1e30	T	A	11: 73,678,616 (GRCm39)	M284K	probably damaging	Het
Or2ag12	T	A	7: 106,276,877 (GRCm39)	N272I	probably damaging	Het
Or4c118	A	T	2: 88,975,078 (GRCm39)	C96*	probably null	Het
Or51k2	A	T	7: 103,596,150 (GRCm39)	I126F	probably damaging	Het
Or51l4	C	T	7: 103,404,527 (GRCm39)	W88*	probably null	Het
Pate6	T	A	9: 35,700,309 (GRCm39)	H92L	probably benign	Het
Pclo	A	G	5: 14,763,487 (GRCm39)	T3987A	unknown	Het
Pik3cg	A	T	12: 32,242,152 (GRCm39)	V986D	probably damaging	Het
Pitpnm1	T	A	19: 4,162,450 (GRCm39)	D1093E	probably damaging	Het
Ppp1r12b	T	C	1: 134,793,651 (GRCm39)	D571G	probably benign	Het
Rfx1	A	G	8: 84,822,126 (GRCm39)	E875G	probably damaging	Het
Rnf145	T	A	11: 44,439,642 (GRCm39)	I146N	probably damaging	Het
Rttn	G	A	18: 89,108,557 (GRCm39)	R1587H	probably benign	Het
Safb	A	G	17: 56,912,821 (GRCm39)	H883R	probably benign	Het
Sdhb	A	G	4: 140,700,260 (GRCm39)	D120G	possibly damaging	Het
Serpine3	A	G	14: 62,902,533 (GRCm39)	N48S	probably damaging	Het
Slc1a7	G	T	4: 107,825,782 (GRCm39)	D14Y	probably benign	Het
Smtnl2	C	T	11: 72,302,183 (GRCm39)	A93T	probably benign	Het
Srpra	T	C	9: 35,124,834 (GRCm39)		probably null	Het
Taf6l	A	G	19: 8,752,866 (GRCm39)		probably null	Het
Tbc1d10b	A	T	7: 126,807,036 (GRCm39)	V167E	probably benign	Het
Tbc1d9	G	A	8: 83,976,139 (GRCm39)	R566H	probably damaging	Het
Tenm3	A	G	8: 48,689,348 (GRCm39)	Y2080H	probably damaging	Het
Tex14	A	G	11: 87,402,431 (GRCm39)	N506S	probably damaging	Het
Thada	G	T	17: 84,617,470 (GRCm39)	P1349T	probably damaging	Het
Tjp1	G	T	7: 64,973,826 (GRCm39)	T476K	probably damaging	Het
Tlr11	A	T	14: 50,598,691 (GRCm39)	T226S	probably benign	Het
Tmem131	G	A	1: 36,843,680 (GRCm39)	Q1394*	probably null	Het
Tmem161a	C	T	8: 70,629,559 (GRCm39)	R58W	probably damaging	Het
Tmem219	T	C	7: 126,496,422 (GRCm39)	S13G	probably benign	Het
Trp53bp1	T	C	2: 121,035,517 (GRCm39)	Y47C	probably damaging	Het
Ttn	T	A	2: 76,731,922 (GRCm39)		probably benign	Het
Ush1g	A	G	11: 115,209,280 (GRCm39)	S305P	probably damaging	Het
Usp37	A	T	1: 74,479,127 (GRCm39)	Y948*	probably null	Het
Vav1	A	T	17: 57,634,697 (GRCm39)	Y805F	probably damaging	Het
Vmn1r59	A	T	7: 5,457,038 (GRCm39)	Y241N	probably damaging	Het
Vmn2r2	T	A	3: 64,034,121 (GRCm39)	Y467F	probably damaging	Het
Vps35l	A	C	7: 118,374,557 (GRCm39)	R352S	probably damaging	Het
Vps54	C	A	11: 21,242,051 (GRCm39)	L389I	probably damaging	Het
Vwa8	G	T	14: 79,162,694 (GRCm39)		probably benign	Het
Wdr19	G	T	5: 65,398,503 (GRCm39)		probably benign	Het
Wnt2b	A	T	3: 104,861,933 (GRCm39)		probably benign	Het
Xirp2	A	G	2: 67,342,039 (GRCm39)	R1427G	possibly damaging	Het
Ylpm1	T	C	12: 85,087,560 (GRCm39)	S1115P	probably damaging	Het
Zfp946	T	A	17: 22,674,406 (GRCm39)	C387S	probably damaging	Het

Other mutations in Sgms1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- AAGTCTTGCCCCACTCCATG -3'
(R):5'- GAAGTGGTTTACTGGTCACCCAAG -3'

Sequencing Primer
(F):5'- CACTCCATGGGATACTGGGAG -3'
(R):5'- CCCAAGAAGGTGGCAGACTG -3'

Posted On

2014-08-25