Mutagenetix > Incidental Mutation

Incidental Mutation 'R7156:Smpd1'

557312

Institutional Source

Beutler Lab

Gene Symbol

Smpd1

Ensembl Gene

ENSMUSG00000037049

Gene Name

sphingomyelin phosphodiesterase 1, acid lysosomal

Synonyms

ASM, aSMase, A-SMase, acid sphingomyelinase, Zn-SMase

MMRRC Submission

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.302) question?

Stock #

R7156 (G1)

Quality Score

149.008

Status

Validated

Chromosome

Chromosomal Location

105554360-105558389 bp(+) (GRCm38)

Type of Mutation

unclassified

DNA Base Change (assembly)

C to T at 105554486 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Gene Model

predicted gene model for transcript(s): [ENSMUST00000046983] [ENSMUST00000081165] [ENSMUST00000186814] [ENSMUST00000187057] [ENSMUST00000188001] [ENSMUST00000188368] [ENSMUST00000189072] [ENSMUST00000189265] [ENSMUST00000189378] [ENSMUST00000190369] [ENSMUST00000191011] [ENSMUST00000191601]

AlphaFold

Q04519

Predicted Effect

probably benign
Transcript: ENSMUST00000046983

SMART Domains

Protein: ENSMUSP00000042187
Gene: ENSMUSG00000037049

Domain	Start	End	E-Value	Type
transmembrane domain	30	52	N/A	INTRINSIC
SapB	85	163	1.05e-7	SMART
low complexity region	177	196	N/A	INTRINSIC
Pfam:Metallophos	197	459	4.4e-21	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000081165

SMART Domains

Protein: ENSMUSP00000079932
Gene: ENSMUSG00000037032

Domain	Start	End	E-Value	Type
low complexity region	146	184	N/A	INTRINSIC
WW	254	285	6.23e-5	SMART
low complexity region	287	299	N/A	INTRINSIC
PTB	365	512	4.16e-38	SMART
PTB	538	667	1.76e-36	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000186814

Predicted Effect

probably benign
Transcript: ENSMUST00000187057

SMART Domains

Protein: ENSMUSP00000139899
Gene: ENSMUSG00000037032

Domain	Start	End	E-Value	Type
WW	31	62	3.7e-7	SMART
low complexity region	64	76	N/A	INTRINSIC
PTB	142	287	3.8e-41	SMART
PTB	313	442	9.5e-39	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000188001

Predicted Effect

probably benign
Transcript: ENSMUST00000188368

SMART Domains

Protein: ENSMUSP00000139788
Gene: ENSMUSG00000037032

Domain	Start	End	E-Value	Type
WW	31	62	3.7e-7	SMART
low complexity region	64	76	N/A	INTRINSIC
PTB	142	289	1.8e-40	SMART
PTB	315	444	9.5e-39	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000189072

SMART Domains

Protein: ENSMUSP00000139575
Gene: ENSMUSG00000037032

Domain	Start	End	E-Value	Type
Pfam:WW	1	24	8.1e-5	PFAM
low complexity region	28	40	N/A	INTRINSIC
PTB	106	253	1.8e-40	SMART
PTB	279	408	9.5e-39	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000189265

SMART Domains

Protein: ENSMUSP00000140137
Gene: ENSMUSG00000037032

Domain	Start	End	E-Value	Type
Pfam:PID	1	34	2.3e-6	PFAM
PTB	63	192	9.5e-39	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000189378

SMART Domains

Protein: ENSMUSP00000140979
Gene: ENSMUSG00000037032

Domain	Start	End	E-Value	Type
low complexity region	146	184	N/A	INTRINSIC
WW	254	285	6.23e-5	SMART
low complexity region	287	299	N/A	INTRINSIC
PTB	365	510	6.86e-39	SMART
PTB	536	665	1.76e-36	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000190369

SMART Domains

Protein: ENSMUSP00000140486
Gene: ENSMUSG00000037032

Domain	Start	End	E-Value	Type
Pfam:WW	1	24	8.1e-5	PFAM
low complexity region	28	40	N/A	INTRINSIC
PTB	106	253	1.8e-40	SMART
PTB	279	408	9.5e-39	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000191011

SMART Domains

Protein: ENSMUSP00000140973
Gene: ENSMUSG00000037032

Domain	Start	End	E-Value	Type
low complexity region	146	184	N/A	INTRINSIC
WW	254	285	6.23e-5	SMART
low complexity region	287	299	N/A	INTRINSIC
PTB	365	510	6.86e-39	SMART
PTB	536	665	1.76e-36	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000191601

SMART Domains

Protein: ENSMUSP00000140116
Gene: ENSMUSG00000037032

Domain	Start	End	E-Value	Type
low complexity region	146	184	N/A	INTRINSIC
WW	254	285	3.7e-7	SMART
low complexity region	287	299	N/A	INTRINSIC
PTB	365	512	1.8e-40	SMART
PTB	538	667	9.5e-39	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000211614

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (81/81)

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 a lysosomal acid sphingomyelinase that converts sphingomyelin to ceramide. The encoded protein also has phospholipase C activity. Defects in this gene are a cause of Niemann-Pick disease type A (NPA) and Niemann-Pick disease type B (NPB). Multiple transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]
PHENOTYPE: Nullizygous mutations cause tremors, ataxia, altered lipid homeostasis, increased foam cell number, Purkinje cell loss and premature death, and may lead to hepatosplenomegaly, hunched posture, reduced weight, abnormal apoptosis, sperm defects, dyspnea, and high susceptibility to bacterial infection. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930433I11Rik	T	C	7: 40,993,858	I317T	possibly damaging	Het
4931406P16Rik	G	T	7: 34,245,708	N582K	possibly damaging	Het
4931409K22Rik	C	T	5: 24,552,650	E150K	probably benign	Het
Acsl5	G	A	19: 55,268,828		probably null	Het
Ahrr	G	A	13: 74,229,916	T136I	probably damaging	Het
AI597479	G	A	1: 43,111,101	D124N	probably damaging	Het
Arap2	G	T	5: 62,604,571	A1604D	probably damaging	Het
Bcl6	G	A	16: 23,966,226	R675*	probably null	Het
Cadps2	T	C	6: 23,688,956	N118S	probably benign	Het
Caskin1	T	A	17: 24,500,683		probably null	Het
Cc2d1a	C	T	8: 84,135,760	V684M	possibly damaging	Het
Ccdc91	T	C	6: 147,534,178	S87P	possibly damaging	Het
Cdr2l	A	G	11: 115,390,966	Q99R	probably benign	Het
Celsr3	T	C	9: 108,838,004	L2066P	possibly damaging	Het
Cep95	A	C	11: 106,809,224	L313F	possibly damaging	Het
Chst10	G	A	1: 38,874,007	T63M	probably damaging	Het
Clrn2	G	A	5: 45,453,916	G36R	probably damaging	Het
Cnn2	T	G	10: 79,994,515	Y273*	probably null	Het
Crtap	T	C	9: 114,378,096	T365A	probably benign	Het
D630045J12Rik	T	C	6: 38,195,029	T735A	possibly damaging	Het
Disp2	C	T	2: 118,791,811	A1008V	probably damaging	Het
Dmrt3	A	G	19: 25,610,953	D52G	probably damaging	Het
Dmrta1	T	G	4: 89,688,463	L52R	probably damaging	Het
Dmrta2	A	G	4: 109,981,988	T311A	probably damaging	Het
Dnm1	T	A	2: 32,340,467	N112Y	probably damaging	Het
Dysf	T	C	6: 84,087,876		probably null	Het
Ep400	A	G	5: 110,685,363	F2034L	unknown	Het
F12	G	A	13: 55,418,497	A494V	probably damaging	Het
Fbp2	A	T	13: 62,841,861	F210L	probably benign	Het
Fbxo31	T	A	8: 121,554,321	Q362L	possibly damaging	Het
Fkbp4	C	T	6: 128,435,824	A95T	probably benign	Het
Frmd6	T	G	12: 70,877,209	C80W	probably damaging	Het
Fsip2	A	G	2: 82,982,741	I3135V	probably benign	Het
Gm597	A	T	1: 28,776,767	M728K	possibly damaging	Het
Guca2b	T	A	4: 119,657,690	E34V	probably damaging	Het
Hdlbp	G	A	1: 93,413,915	T974I	probably damaging	Het
Hsdl2	T	A	4: 59,617,653	M460K	possibly damaging	Het
Ift172	C	T	5: 31,272,075	V581M	probably damaging	Het
Ift74	A	G	4: 94,660,952	K313R	possibly damaging	Het
Ints4	T	A	7: 97,535,286		probably null	Het
Kif21b	A	C	1: 136,147,824	T230P	probably damaging	Het
Kit	A	T	5: 75,615,374	Y272F	probably benign	Het
Krt77	G	A	15: 101,865,496	T241M	probably benign	Het
Lce1j	T	A	3: 92,789,184	S96C	unknown	Het
Marveld3	T	A	8: 109,948,188	D332V	probably damaging	Het
Matr3	G	T	18: 35,572,921	V300F	probably damaging	Het
Mical1	T	A	10: 41,485,257		probably null	Het
Mslnl	T	A	17: 25,743,210	V194E	probably benign	Het
Mug1	C	A	6: 121,880,905	T1119K	probably damaging	Het
Mug1	C	T	6: 121,884,343	P1308S	probably damaging	Het
Neb	C	A	2: 52,305,283		probably null	Het
Neo1	T	A	9: 58,902,923	T1082S	probably damaging	Het
Nkx6-2	C	T	7: 139,582,129		probably null	Het
Olfr1065	T	A	2: 86,445,308	I225L	probably damaging	Het
Olfr981	T	C	9: 40,023,230	I279T	probably benign	Het
Orc1	A	T	4: 108,595,459	E177V	probably benign	Het
Parp1	G	A	1: 180,599,064	V924I	possibly damaging	Het
Pax2	A	T	19: 44,788,859	I165F	probably benign	Het
Pnma2	C	T	14: 66,916,531	P135S	probably benign	Het
Ranbp17	A	G	11: 33,297,420	I718T	probably damaging	Het
Rbm25	T	A	12: 83,664,191	D359E	unknown	Het
Rgs3	T	C	4: 62,617,126	L194P	probably damaging	Het
Serpinb6b	A	G	13: 32,971,615	I104V	probably benign	Het
Smg9	A	G	7: 24,420,861	D420G	probably benign	Het
Snx17	T	A	5: 31,197,348	M318K	probably damaging	Het
Stard10	G	A	7: 101,346,051	D337N	probably damaging	Het
Tex14	A	G	11: 87,484,719	T103A	probably damaging	Het
Tle1	A	G	4: 72,170,716	S97P	probably benign	Het
Tnfrsf8	T	A	4: 145,315,084	M1L	unknown	Het
Traf3ip2	T	C	10: 39,626,177	L107P	possibly damaging	Het
Trpc7	A	T	13: 56,789,766	S626T	possibly damaging	Het
Ubl7	T	A	9: 57,929,756	I350N	probably damaging	Het
Ubr3	T	A	2: 70,021,623	I1878N	probably damaging	Het
Usp24	G	T	4: 106,387,919		probably null	Het
Vcan	A	T	13: 89,689,110	S2772T	possibly damaging	Het
Vmn2r79	T	C	7: 87,037,643	V744A	probably damaging	Het
Wbp2nl	T	C	15: 82,305,702	S32P	probably damaging	Het
Wwc1	A	G	11: 35,897,374		probably null	Het
Zfp629	C	T	7: 127,612,291	W115*	probably null	Het

Other mutations in Smpd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00493:Smpd1	APN	7	105556641	missense	probably damaging	0.99
IGL01147:Smpd1	APN	7	105555736	missense	probably damaging	1.00
IGL01526:Smpd1	APN	7	105554775	missense	probably benign	0.01
IGL01541:Smpd1	APN	7	105555826	missense	possibly damaging	0.48
IGL01619:Smpd1	APN	7	105555342	missense	possibly damaging	0.89
IGL01924:Smpd1	APN	7	105555448	missense	probably benign	0.01
IGL03004:Smpd1	APN	7	105556674	missense	possibly damaging	0.82
R0782:Smpd1	UTSW	7	105555343	missense	possibly damaging	0.80
R1445:Smpd1	UTSW	7	105556674	missense	possibly damaging	0.82
R1489:Smpd1	UTSW	7	105556554	splice site	probably null
R3683:Smpd1	UTSW	7	105555402	missense	probably damaging	1.00
R3685:Smpd1	UTSW	7	105555402	missense	probably damaging	1.00
R3977:Smpd1	UTSW	7	105555901	missense	probably benign	0.29
R4850:Smpd1	UTSW	7	105555985	missense	probably benign
R5084:Smpd1	UTSW	7	105556978	missense	probably damaging	1.00
R6316:Smpd1	UTSW	7	105555502	missense	probably benign	0.19
R6429:Smpd1	UTSW	7	105556928	missense	probably damaging	1.00
R6672:Smpd1	UTSW	7	105555273	missense	probably benign
R7883:Smpd1	UTSW	7	105556985	missense	probably damaging	1.00
R8261:Smpd1	UTSW	7	105555313	missense	probably benign	0.01
R9287:Smpd1	UTSW	7	105555235	missense	probably benign	0.14
R9406:Smpd1	UTSW	7	105554543	missense	possibly damaging	0.62
R9461:Smpd1	UTSW	7	105555582	missense	probably damaging	1.00
R9496:Smpd1	UTSW	7	105555995	critical splice donor site	probably null
X0021:Smpd1	UTSW	7	105557645	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGCTTGTCTCTACCGAGGTC -3'
(R):5'- ACCGTGGAGTCAAACAGAGC -3'

Sequencing Primer
(F):5'- GTCTCTACCGAGGTCACCTAC -3'
(R):5'- TGGAGTCAAACAGAGCCAGAACC -3'

Posted On

2019-06-26