Mutagenetix > Incidental Mutation

Incidental Mutation 'R5383:Smpd2'

424853

Institutional Source

Beutler Lab

Gene Symbol

Smpd2

Ensembl Gene

ENSMUSG00000019822

Gene Name

sphingomyelin phosphodiesterase 2, neutral

Synonyms

nSMase

MMRRC Submission

042958-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5383 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

41363168-41366410 bp(-) (GRCm39)

Type of Mutation

intron

DNA Base Change (assembly)

C to T at 41364698 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000115461 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000019965] [ENSMUST00000019967] [ENSMUST00000099934] [ENSMUST00000105507] [ENSMUST00000119962] [ENSMUST00000155411] [ENSMUST00000126436]

AlphaFold

O70572

Predicted Effect

probably benign
Transcript: ENSMUST00000019965

SMART Domains

Protein: ENSMUSP00000019965
Gene: ENSMUSG00000019822

Domain	Start	End	E-Value	Type
Pfam:Exo_endo_phos	11	272	3.9e-24	PFAM
transmembrane domain	322	344	N/A	INTRINSIC
transmembrane domain	353	375	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000019967

SMART Domains

Protein: ENSMUSP00000019967
Gene: ENSMUSG00000019823

Domain	Start	End	E-Value	Type
Pfam:FAD_binding_3	84	140	5.5e-8	PFAM
Pfam:FAD_binding_2	86	125	6.1e-6	PFAM
low complexity region	160	171	N/A	INTRINSIC
CH	509	606	4.18e-13	SMART
low complexity region	649	666	N/A	INTRINSIC
LIM	682	736	2.07e-3	SMART
low complexity region	766	785	N/A	INTRINSIC
low complexity region	787	803	N/A	INTRINSIC
low complexity region	855	877	N/A	INTRINSIC
DUF3585	912	1048	3.07e-44	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000099934

SMART Domains

Protein: ENSMUSP00000097519
Gene: ENSMUSG00000019823

Domain	Start	End	E-Value	Type
PDB:2C4C\|B	1	86	5e-49	PDB
low complexity region	87	98	N/A	INTRINSIC
PDB:2C4C\|B	99	416	N/A	PDB
CH	436	533	4.18e-13	SMART
low complexity region	576	593	N/A	INTRINSIC
LIM	609	663	2.07e-3	SMART
low complexity region	693	712	N/A	INTRINSIC
low complexity region	714	730	N/A	INTRINSIC
low complexity region	782	804	N/A	INTRINSIC
DUF3585	839	975	3.07e-44	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000105507

SMART Domains

Protein: ENSMUSP00000101146
Gene: ENSMUSG00000078451

Domain	Start	End	E-Value	Type
low complexity region	20	33	N/A	INTRINSIC
Pfam:Pro_isomerase	147	310	1.3e-41	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000119962

SMART Domains

Protein: ENSMUSP00000113783
Gene: ENSMUSG00000019823

Domain	Start	End	E-Value	Type
Pfam:FAD_binding_3	84	140	7.2e-8	PFAM
Pfam:FAD_binding_2	86	125	3.8e-6	PFAM
low complexity region	160	171	N/A	INTRINSIC
CH	509	606	4.18e-13	SMART
low complexity region	649	666	N/A	INTRINSIC
LIM	682	736	2.07e-3	SMART
low complexity region	766	785	N/A	INTRINSIC
low complexity region	787	803	N/A	INTRINSIC
low complexity region	855	877	N/A	INTRINSIC
DUF3585	912	1048	3.07e-44	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000122997

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123798

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126833

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134010

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138657

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141542

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147367

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125099

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143470

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132170

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147738

Predicted Effect

probably benign
Transcript: ENSMUST00000155411

SMART Domains

Protein: ENSMUSP00000115461
Gene: ENSMUSG00000019822

Domain	Start	End	E-Value	Type
SCOP:d2dnja_	9	81	2e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000215608

Predicted Effect

probably benign
Transcript: ENSMUST00000126436

SMART Domains

Protein: ENSMUSP00000114969
Gene: ENSMUSG00000019823

Domain	Start	End	E-Value	Type
Pfam:FAD_binding_3	84	140	1.1e-7	PFAM
Pfam:FAD_binding_2	86	125	3.2e-6	PFAM
low complexity region	160	171	N/A	INTRINSIC
CH	509	606	4.18e-13	SMART
low complexity region	649	666	N/A	INTRINSIC
LIM	682	736	2.07e-3	SMART
low complexity region	766	785	N/A	INTRINSIC
low complexity region	787	803	N/A	INTRINSIC
low complexity region	855	877	N/A	INTRINSIC

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.5%
20x: 96.0%

Validation Efficiency

97% (61/63)

MGI Phenotype

FUNCTION: This gene encodes a protein with similarity to the human nSMase1 protein. In humans, the nSMase1 protein was initially identified as a sphingomyelinase based on sequence similarity between bacterial sphingomyelinases and a yeast protein. Subsequent studies showed that its biological function is less likely to be as a sphingomyelinase and instead as a lysophospholipase. [provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for a knock-out allele are phenotypically normal, have a normal lifespan, and display neither lipid accumulation nor changes in sphingomyelin levels despite grossly reduced enzyme activity in all organs except brain. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700010I14Rik	A	T	17: 9,211,532 (GRCm39)	Y227F	possibly damaging	Het
Aadac	T	C	3: 59,943,496 (GRCm39)		probably benign	Het
Abl2	G	A	1: 156,469,802 (GRCm39)	G918E	possibly damaging	Het
Acvr1c	T	C	2: 58,177,747 (GRCm39)	T241A	probably damaging	Het
Adck1	T	C	12: 88,422,373 (GRCm39)	V328A	probably benign	Het
Ano6	A	G	15: 95,813,918 (GRCm39)	I279V	probably benign	Het
AW551984	T	A	9: 39,501,994 (GRCm39)	Y704F	probably benign	Het
C1s1	T	C	6: 124,511,360 (GRCm39)	D321G	probably damaging	Het
Cacna1d	T	A	14: 29,767,236 (GRCm39)	D1910V	possibly damaging	Het
Cdh5	A	G	8: 104,864,479 (GRCm39)	Q480R	probably benign	Het
Cdhr1	C	T	14: 36,810,964 (GRCm39)	V266M	possibly damaging	Het
Cdk5rap1	A	T	2: 154,192,755 (GRCm39)	V414D	possibly damaging	Het
Ctdnep1	T	A	11: 69,875,222 (GRCm39)		probably benign	Het
Cyfip2	T	C	11: 46,168,918 (GRCm39)	M212V	possibly damaging	Het
D130043K22Rik	G	A	13: 25,041,397 (GRCm39)	S273N	probably benign	Het
Ddi2	A	G	4: 141,412,163 (GRCm39)	S250P	probably damaging	Het
Dennd1b	A	G	1: 139,095,409 (GRCm39)	T486A	probably benign	Het
Disc1	A	G	8: 125,862,196 (GRCm39)	T523A	probably damaging	Het
Dmbx1	A	G	4: 115,775,342 (GRCm39)	S313P	probably damaging	Het
Dmpk	C	G	7: 18,821,944 (GRCm39)	L301V	probably benign	Het
Dnah11	T	C	12: 118,049,432 (GRCm39)	E1664G	probably damaging	Het
Dpysl3	A	T	18: 43,571,103 (GRCm39)	V57E	probably damaging	Het
Fam98a	C	T	17: 75,845,576 (GRCm39)	G390E	unknown	Het
Hook3	C	A	8: 26,609,017 (GRCm39)	R9L	probably benign	Het
Igkv4-80	A	C	6: 68,993,649 (GRCm39)	S81A	probably benign	Het
Impg2	A	G	16: 56,063,989 (GRCm39)	D298G	probably benign	Het
Inf2	T	A	12: 112,566,579 (GRCm39)	V48D	probably damaging	Het
Itprid1	T	A	6: 55,955,275 (GRCm39)	L961H	probably benign	Het
Kcnh1	G	A	1: 192,187,999 (GRCm39)	G820D	probably benign	Het
Lsm14a	C	T	7: 34,088,789 (GRCm39)	A39T	possibly damaging	Het
Muc2	T	C	7: 141,307,456 (GRCm39)	C804R	probably damaging	Het
Nim1k	C	T	13: 120,189,335 (GRCm39)	V25M	probably benign	Het
Or11g25	T	A	14: 50,723,509 (GRCm39)	L198*	probably null	Het
Or4a73	T	C	2: 89,421,457 (GRCm39)	M1V	probably null	Het
Or5b122	T	A	19: 13,563,439 (GRCm39)	M257K	probably damaging	Het
Or6c68	A	G	10: 129,158,205 (GRCm39)	T238A	probably damaging	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Phf8-ps	T	C	17: 33,284,231 (GRCm39)	D857G	probably benign	Het
Pitrm1	T	A	13: 6,627,468 (GRCm39)	H856Q	probably damaging	Het
Pkd1	T	C	17: 24,793,349 (GRCm39)	C1679R	probably benign	Het
Pkp4	T	A	2: 59,140,617 (GRCm39)	L441*	probably null	Het
Ppp4r4	T	C	12: 103,550,427 (GRCm39)	F284L	probably benign	Het
Ptprt	T	A	2: 161,539,969 (GRCm39)	K769M	probably damaging	Het
Rbm12	G	T	2: 155,945,285 (GRCm39)		probably benign	Het
Rpf1	T	C	3: 146,225,146 (GRCm39)	D94G	possibly damaging	Het
Scap	G	T	9: 110,203,597 (GRCm39)	K310N	probably damaging	Het
Sp110	TC	TCC	1: 85,519,290 (GRCm39)		probably null	Het
Specc1l	T	A	10: 75,082,539 (GRCm39)	I662N	possibly damaging	Het
Sptan1	T	A	2: 29,901,340 (GRCm39)	V1496D	probably damaging	Het
Srrm4	T	C	5: 116,609,319 (GRCm39)		probably benign	Het
Taf2	A	G	15: 54,912,815 (GRCm39)	I515T	possibly damaging	Het
Tdrd3	C	T	14: 87,718,227 (GRCm39)	Q203*	probably null	Het
Tfap2b	A	T	1: 19,296,722 (GRCm39)	M222L	probably benign	Het
Tmem43	G	A	6: 91,450,872 (GRCm39)	A2T	probably benign	Het
Trav9-1	T	A	14: 53,725,833 (GRCm39)	I49N	probably benign	Het
Trim23	T	G	13: 104,335,205 (GRCm39)	N410K	probably damaging	Het
Ttbk1	T	C	17: 46,778,342 (GRCm39)	T567A	probably damaging	Het
Unc79	A	G	12: 103,070,886 (GRCm39)	N1081S	possibly damaging	Het
Zfp451	A	C	1: 33,852,887 (GRCm39)	I9R	probably damaging	Het
Zfp563	T	A	17: 33,323,681 (GRCm39)	M92K	probably benign	Het
Zfp618	G	A	4: 63,013,729 (GRCm39)	G198D	probably benign	Het
Zfp637	G	T	6: 117,820,270 (GRCm39)		probably benign	Het

Other mutations in Smpd2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01581:Smpd2	APN	10	41,365,524 (GRCm39)	missense	possibly damaging	0.52
IGL02797:Smpd2	APN	10	41,364,074 (GRCm39)	missense	possibly damaging	0.90
clumsy	UTSW	10	41,363,967 (GRCm39)	splice site	probably null
R1170:Smpd2	UTSW	10	41,364,728 (GRCm39)	critical splice donor site	probably null
R1832:Smpd2	UTSW	10	41,364,232 (GRCm39)	missense	probably benign	0.01
R5388:Smpd2	UTSW	10	41,363,967 (GRCm39)	splice site	probably null
R5905:Smpd2	UTSW	10	41,365,344 (GRCm39)	missense	probably damaging	1.00
R6028:Smpd2	UTSW	10	41,365,344 (GRCm39)	missense	probably damaging	1.00
R6833:Smpd2	UTSW	10	41,364,442 (GRCm39)	missense	probably damaging	0.98
R7440:Smpd2	UTSW	10	41,365,012 (GRCm39)	missense	probably benign	0.13
R7505:Smpd2	UTSW	10	41,363,350 (GRCm39)	missense	probably benign	0.09
R8869:Smpd2	UTSW	10	41,365,301 (GRCm39)	missense	probably benign
R9200:Smpd2	UTSW	10	41,363,561 (GRCm39)	missense	probably benign	0.03
R9275:Smpd2	UTSW	10	41,363,685 (GRCm39)	missense	probably benign
R9621:Smpd2	UTSW	10	41,364,283 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- CTTCTGTCGGCTGTACTCAG -3'
(R):5'- ATCCTTGCTAACACAGACTGG -3'

Sequencing Primer
(F):5'- CATGTAGCTAAAGTGGAATAGGTG -3'
(R):5'- TGCTAACACAGACTGGACGCAG -3'

Posted On

2016-08-04