Mutagenetix > Incidental Mutation

Incidental Mutation 'R8507:Sgms1'

655674

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

067843-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.931) question?

Stock #

R8507 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

32100127-32367114 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 32137109 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 152 (F152L)

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

probably benign
Transcript: ENSMUST00000099514
AA Change: F152L

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000097114
Gene: ENSMUSG00000040451
AA Change: F152L

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

probably benign
Transcript: ENSMUST00000134415
AA Change: F152L

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000115785
Gene: ENSMUSG00000040451
AA Change: F152L

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

probably benign
Transcript: ENSMUST00000142618
AA Change: F152L

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000117336
Gene: ENSMUSG00000040451
AA Change: F152L

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

probably benign
Transcript: ENSMUST00000151289
AA Change: F152L

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000123395
Gene: ENSMUSG00000040451
AA Change: F152L

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

possibly damaging
Transcript: ENSMUST00000152340
AA Change: F152L

PolyPhen 2 Score 0.580 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000119869
Gene: ENSMUSG00000040451
AA Change: F152L

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam7	A	G	14: 68,763,773 (GRCm39)	C126R	probably damaging	Het
Agpat5	G	A	8: 18,928,043 (GRCm39)	V203I	possibly damaging	Het
Ankrd12	T	A	17: 66,293,904 (GRCm39)	R510*	probably null	Het
Anxa6	C	T	11: 54,904,696 (GRCm39)	A22T	probably benign	Het
Barx2	A	T	9: 31,770,309 (GRCm39)	L73Q	probably damaging	Het
BC024139	T	C	15: 76,004,333 (GRCm39)	K702R	possibly damaging	Het
Cc2d1a	T	C	8: 84,861,605 (GRCm39)	K739R	probably benign	Het
Cdk12	A	G	11: 98,141,111 (GRCm39)	T1451A	unknown	Het
Chd7	A	G	4: 8,858,675 (GRCm39)	E2367G	probably damaging	Het
Cp	A	G	3: 20,025,193 (GRCm39)	Y384C	probably damaging	Het
Dnah14	T	A	1: 181,468,979 (GRCm39)	W1270R	probably benign	Het
Dyrk2	G	T	10: 118,696,567 (GRCm39)	S230R	probably damaging	Het
Epn3	A	T	11: 94,384,602 (GRCm39)	S290R	probably damaging	Het
Fas	C	T	19: 34,304,626 (GRCm39)	R296C	probably benign	Het
Fmnl1	A	T	11: 103,084,859 (GRCm39)	N659I	unknown	Het
Gas8	T	C	8: 124,257,777 (GRCm39)		probably null	Het
Gpr156	A	G	16: 37,768,598 (GRCm39)	T40A	probably benign	Het
Hey1	G	C	3: 8,729,836 (GRCm39)	A207G	probably benign	Het
Htr3b	C	A	9: 48,876,177 (GRCm39)		probably benign	Het
Itgal	C	T	7: 126,928,607 (GRCm39)	T1044I	probably benign	Het
Itprid2	A	G	2: 79,475,208 (GRCm39)	Q389R	probably benign	Het
Kcnip4	T	G	5: 48,639,997 (GRCm39)	D38A	possibly damaging	Het
Kcnma1	G	T	14: 23,641,706 (GRCm39)	Q216K	probably benign	Het
Kdsr	T	A	1: 106,671,400 (GRCm39)	E203V	probably null	Het
Lrp1b	T	C	2: 41,298,387 (GRCm39)	E999G		Het
Malt1	T	A	18: 65,603,594 (GRCm39)	W577R	probably damaging	Het
Mroh2b	A	C	15: 4,978,572 (GRCm39)	T1373P	probably damaging	Het
Mymk	A	G	2: 26,952,712 (GRCm39)		probably null	Het
Myo1f	T	A	17: 33,816,992 (GRCm39)	H707Q	probably benign	Het
Ncam2	C	A	16: 81,309,867 (GRCm39)	H452Q	possibly damaging	Het
Ndrg4	A	G	8: 96,404,975 (GRCm39)	M1V	probably null	Het
Nps	C	T	7: 134,874,079 (GRCm39)	S83L	probably damaging	Het
Nup155	T	A	15: 8,177,044 (GRCm39)	Y1040*	probably null	Het
Or1j15	T	C	2: 36,459,443 (GRCm39)	Y278H	probably damaging	Het
Or2ak4	C	T	11: 58,648,985 (GRCm39)	Q165*	probably null	Het
Or4f7	T	C	2: 111,645,051 (GRCm39)	T7A	probably benign	Het
Or5h22	C	T	16: 58,895,243 (GRCm39)	V67M	possibly damaging	Het
Pak1ip1	G	A	13: 41,162,770 (GRCm39)	R191Q	probably benign	Het
Pcdh17	G	A	14: 84,683,384 (GRCm39)		probably benign	Het
Pcdhgc5	G	T	18: 37,952,945 (GRCm39)	R73L	probably benign	Het
Peg10	C	CTCA	6: 4,756,453 (GRCm39)		probably benign	Het
Plat	G	T	8: 23,262,248 (GRCm39)	G91W	probably damaging	Het
Plscr4	C	T	9: 92,372,843 (GRCm39)	R322*	probably null	Het
Plxnd1	A	T	6: 115,943,866 (GRCm39)	N1144K	probably damaging	Het
Ppp1r1b	G	T	11: 98,246,310 (GRCm39)	E133D	probably damaging	Het
Ptpn13	A	G	5: 103,705,815 (GRCm39)	E1396G	probably damaging	Het
Reps1	T	C	10: 17,970,218 (GRCm39)	S272P	probably damaging	Het
Ric8b	T	C	10: 84,816,039 (GRCm39)	V430A	probably damaging	Het
Septin10	A	T	10: 59,012,825 (GRCm39)	N264K	possibly damaging	Het
Snapc1	C	A	12: 74,011,506 (GRCm39)	F57L	probably damaging	Het
Spidr	A	G	16: 15,786,540 (GRCm39)	L401P	probably damaging	Het
Spn	C	T	7: 126,735,728 (GRCm39)	V260M	probably damaging	Het
Sptan1	G	A	2: 29,916,596 (GRCm39)	A2095T	probably damaging	Het
Tbc1d15	A	G	10: 115,038,407 (GRCm39)		probably null	Het
Thsd7b	T	A	1: 129,605,790 (GRCm39)	F510L	probably benign	Het
Trpm5	T	A	7: 142,632,050 (GRCm39)	I920F	probably damaging	Het
Tspear	C	A	10: 77,710,898 (GRCm39)	H507N	probably benign	Het
Vmn2r108	T	A	17: 20,683,195 (GRCm39)	K670*	probably null	Het
Vmn2r75	A	T	7: 85,797,685 (GRCm39)	C709*	probably null	Het
Wdfy3	G	T	5: 102,020,767 (GRCm39)	S2494R	probably benign	Het
Zfp456	A	T	13: 67,515,108 (GRCm39)	F199L	probably damaging	Het
Zfp830	A	G	11: 82,655,529 (GRCm39)	Q111R	probably benign	Het
Znrf1	G	A	8: 112,263,842 (GRCm39)	A24T	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
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
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
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'- CCTTCATGGCTGGATCTCAAG -3'
(R):5'- TGGCGTTGACATTCCCAACC -3'

Sequencing Primer
(F):5'- CATGGCTGGATCTCAAGAGTGTTTAC -3'
(R):5'- GTTGACATTCCCAACCCCGATG -3'

Posted On

2020-10-20