Mutagenetix > Incidental Mutation

Incidental Mutation 'R7382:Sgms1'

572838

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

045464-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.925) question?

Stock #

R7382 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

32100127-32367114 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 32137182 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 128 (E128G)

Ref Sequence

ENSEMBL: ENSMUSP00000097114 (fasta)

Gene Model

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

AlphaFold

Q8VCQ6

PDB Structure

Solution structure of the sam-domain of mouse phosphatidyl ceramidecholinephosphotransferase 1 [SOLUTION NMR]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000099514
AA Change: E128G

PolyPhen 2 Score 0.680 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000097114
Gene: ENSMUSG00000040451
AA Change: E128G

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

possibly damaging
Transcript: ENSMUST00000134415
AA Change: E128G

PolyPhen 2 Score 0.798 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000115785
Gene: ENSMUSG00000040451
AA Change: E128G

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

possibly damaging
Transcript: ENSMUST00000142618
AA Change: E128G

PolyPhen 2 Score 0.680 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000117336
Gene: ENSMUSG00000040451
AA Change: E128G

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

possibly damaging
Transcript: ENSMUST00000151289
AA Change: E128G

PolyPhen 2 Score 0.680 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000123395
Gene: ENSMUSG00000040451
AA Change: E128G

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: ENSMUST00000151822

Predicted Effect

probably benign
Transcript: ENSMUST00000152340
AA Change: E128G

PolyPhen 2 Score 0.215 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000119869
Gene: ENSMUSG00000040451
AA Change: E128G

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

Meta Mutation Damage Score

0.0743

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

99% (77/78)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610008E11Rik	A	T	10: 78,903,103 (GRCm39)	H404Q	probably damaging	Het
Aadacl2fm2	T	A	3: 59,651,037 (GRCm39)	M53K	probably benign	Het
Adam8	T	A	7: 139,570,020 (GRCm39)	T82S	possibly damaging	Het
Adgrl2	T	G	3: 148,522,919 (GRCm39)	Q435P		Het
Ahr	A	T	12: 35,554,514 (GRCm39)	M535K	probably damaging	Het
Akap6	A	G	12: 53,188,954 (GRCm39)	I2123V	probably benign	Het
Ankrd2	G	T	19: 42,033,411 (GRCm39)	G318C		Het
Ap4e1	T	A	2: 126,850,822 (GRCm39)		probably null	Het
Atp8a2	G	A	14: 59,892,043 (GRCm39)	P1102S	probably benign	Het
Cacna2d4	C	T	6: 119,216,048 (GRCm39)	S105F	probably damaging	Het
Cad	C	A	5: 31,233,173 (GRCm39)	P1872T	probably benign	Het
Catsperg1	A	G	7: 28,904,269 (GRCm39)	F251L	probably benign	Het
Ccdc18	C	A	5: 108,286,873 (GRCm39)	Q136K	probably damaging	Het
Cd163	A	G	6: 124,288,271 (GRCm39)		probably null	Het
Cd209d	A	T	8: 3,927,965 (GRCm39)	Y46*	probably null	Het
Cdk5rap2	A	T	4: 70,208,262 (GRCm39)	M728K	probably benign	Het
Cdon	A	G	9: 35,389,944 (GRCm39)	D866G	probably damaging	Het
Cenpl	A	G	1: 160,906,031 (GRCm39)	H135R	probably benign	Het
Cep20	TTGTG	TTG	16: 14,118,009 (GRCm39)		probably null	Het
Clstn2	A	T	9: 97,681,451 (GRCm39)	L63*	probably null	Het
Cpeb4	A	G	11: 31,822,828 (GRCm39)	T181A	probably damaging	Het
Dlgap1	A	G	17: 71,094,169 (GRCm39)	E830G	probably damaging	Het
Endou	T	A	15: 97,616,807 (GRCm39)	K239*	probably null	Het
Ezh2	T	C	6: 47,528,770 (GRCm39)	N263S	possibly damaging	Het
Fbxw2	T	C	2: 34,697,314 (GRCm39)	D351G	probably benign	Het
Fer1l4	A	T	2: 155,862,669 (GRCm39)	Y1720*	probably null	Het
Fmo9	A	T	1: 166,491,229 (GRCm39)		probably null	Het
Frmpd1	T	A	4: 45,278,880 (GRCm39)	V535E	probably benign	Het
Fxr2	T	C	11: 69,532,382 (GRCm39)	V139A	probably benign	Het
Gpr180	T	G	14: 118,400,035 (GRCm39)	V401G	possibly damaging	Het
Heatr5b	G	T	17: 79,110,936 (GRCm39)	R971S	possibly damaging	Het
Igkv8-34	C	A	6: 70,021,103 (GRCm39)	A120S	probably benign	Het
Inpp5b	T	A	4: 124,645,370 (GRCm39)	H219Q	probably benign	Het
Itprid1	G	T	6: 55,955,404 (GRCm39)	G1004V	probably benign	Het
Kremen2	T	C	17: 23,962,526 (GRCm39)		probably null	Het
Mael	G	A	1: 166,029,167 (GRCm39)	P419S	probably benign	Het
Map1a	A	G	2: 121,121,266 (GRCm39)	T102A	probably damaging	Het
Mfsd2a	A	T	4: 122,845,916 (GRCm39)	I119N	possibly damaging	Het
Muc5b	T	C	7: 141,412,685 (GRCm39)	V1877A	unknown	Het
Myo5c	A	C	9: 75,211,332 (GRCm39)	S1733R	probably damaging	Het
Nelfcd	T	C	2: 174,265,176 (GRCm39)	V248A	probably benign	Het
Npc1	A	T	18: 12,334,763 (GRCm39)	I663N	probably damaging	Het
Olig3	T	A	10: 19,232,413 (GRCm39)	S13T	unknown	Het
Or1j17	G	T	2: 36,578,046 (GRCm39)	E11*	probably null	Het
Or8k39	T	C	2: 86,563,129 (GRCm39)	I276V	probably benign	Het
Piezo2	A	C	18: 63,150,590 (GRCm39)		probably null	Het
Pkd1l2	G	T	8: 117,781,610 (GRCm39)	L812M	possibly damaging	Het
Plcd1	G	A	9: 118,903,759 (GRCm39)	T387I	probably damaging	Het
Ppara	C	T	15: 85,671,429 (GRCm39)	S110L	probably damaging	Het
Ranbp9	C	T	13: 43,578,590 (GRCm39)	R161Q	probably damaging	Het
Rufy2	G	T	10: 62,833,748 (GRCm39)	R270L	probably benign	Het
Septin12	C	T	16: 4,806,346 (GRCm39)	E272K	probably damaging	Het
Sh3bgr	G	A	16: 96,007,093 (GRCm39)	S21N	probably benign	Het
Sil1	A	T	18: 35,458,466 (GRCm39)	D176E	probably benign	Het
Slc13a2	A	T	11: 78,295,621 (GRCm39)	Y82N	probably damaging	Het
Slc41a1	C	T	1: 131,774,370 (GRCm39)	P479L	probably damaging	Het
Smarca4	A	G	9: 21,570,229 (GRCm39)	K744R	probably damaging	Het
Stxbp1	T	C	2: 32,688,180 (GRCm39)	D495G	probably damaging	Het
Sugp2	T	C	8: 70,695,494 (GRCm39)	S156P	probably benign	Het
Syt3	A	T	7: 44,042,170 (GRCm39)	D343V	probably damaging	Het
Tbl3	G	T	17: 24,924,265 (GRCm39)	T164N	probably benign	Het
Tbpl2	A	T	2: 23,977,326 (GRCm39)		probably null	Het
Tcf7l2	T	A	19: 55,915,172 (GRCm39)	W461R	unknown	Het
Tmprss11c	A	T	5: 86,379,723 (GRCm39)	F395Y	probably benign	Het
Tnc	A	T	4: 63,932,280 (GRCm39)	Y711*	probably null	Het
Tnpo2	G	A	8: 85,776,748 (GRCm39)	R485H	probably damaging	Het
Ttc41	A	G	10: 86,612,374 (GRCm39)	K1216E	probably damaging	Het
Ube2q2	A	C	9: 55,070,298 (GRCm39)	D80A	probably damaging	Het
Ube2u	A	T	4: 100,389,379 (GRCm39)	K227*	probably null	Het
Uhrf2	T	C	19: 30,048,788 (GRCm39)	Y265H	possibly damaging	Het
Vmn1r208	T	G	13: 22,956,756 (GRCm39)	Y247S	probably damaging	Het
Vmn2r27	A	G	6: 124,174,276 (GRCm39)	C525R	probably damaging	Het
Vps13a	T	C	19: 16,596,849 (GRCm39)	T3090A	probably damaging	Het
Whrn	T	C	4: 63,336,573 (GRCm39)	K674R	probably benign	Het
Zfp202	G	T	9: 40,122,801 (GRCm39)	R521I	probably damaging	Het
Zfp433	T	C	10: 81,556,659 (GRCm39)	V387A	probably benign	Het
Zpld1	T	C	16: 55,067,046 (GRCm39)		probably null	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
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
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'- AAATAGCCAGAGTCCTACAAGG -3'
(R):5'- AGACCCTGAAGATGGAGCAC -3'

Sequencing Primer
(F):5'- CAAGGATCATGCCGTTAATTTCGC -3'
(R):5'- TGGAGCACCATATGGAAGCAC -3'

Posted On

2019-09-13