Mutagenetix > Incidental Mutation

Incidental Mutation 'R8869:Smpd2'

676149

Institutional Source

Beutler Lab

Gene Symbol

Smpd2

Ensembl Gene

ENSMUSG00000019822

Gene Name

sphingomyelin phosphodiesterase 2, neutral

Synonyms

nSMase

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8869 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

41363168-41366410 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 41365301 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 65 (L65P)

Ref Sequence

ENSEMBL: ENSMUSP00000019965 (fasta)

Gene Model

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

AlphaFold

O70572

Predicted Effect

probably benign
Transcript: ENSMUST00000019965
AA Change: L65P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000019965
Gene: ENSMUSG00000019822
AA Change: L65P

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

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

Predicted Effect

probably benign
Transcript: ENSMUST00000155411
AA Change: L65P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000115461
Gene: ENSMUSG00000019822
AA Change: L65P

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsl5	G	A	19: 55,266,523 (GRCm39)	R114Q	possibly damaging	Het
Atp1a4	C	T	1: 172,054,690 (GRCm39)	V980I	probably benign	Het
Bltp1	T	A	3: 37,013,007 (GRCm39)	C1895S	probably damaging	Het
Brd1	A	T	15: 88,614,729 (GRCm39)	D55E	probably benign	Het
Cachd1	A	G	4: 100,809,280 (GRCm39)	D255G	probably benign	Het
Ccdc168	A	T	1: 44,097,425 (GRCm39)	D1224E	possibly damaging	Het
Ces2f	C	A	8: 105,676,704 (GRCm39)	P133T	probably damaging	Het
Cfap251	A	T	5: 123,460,505 (GRCm39)	M1156L	possibly damaging	Het
Clock	GGCTGCTGCTGCTGCTGCTGCTGCTG	GGCTGCTGCTGCTGCTGCTGCTG	5: 76,374,889 (GRCm39)		probably benign	Het
Cyp4f37	A	T	17: 32,844,096 (GRCm39)	I67F	probably benign	Het
Dbf4	T	C	5: 8,448,656 (GRCm39)	I84V		Het
Dcc	T	C	18: 71,511,755 (GRCm39)	T887A	probably benign	Het
Dhdh	G	T	7: 45,137,536 (GRCm39)	N50K	probably benign	Het
Dnah7c	A	T	1: 46,671,504 (GRCm39)	E1631V	probably damaging	Het
Dusp23	A	G	1: 172,460,293 (GRCm39)	C53R	possibly damaging	Het
Efcab6	G	A	15: 83,928,432 (GRCm39)	S54L	probably damaging	Het
Fcamr	T	C	1: 130,739,335 (GRCm39)	F212L	probably damaging	Het
Gfap	G	C	11: 102,787,810 (GRCm39)	A45G	probably benign	Het
Grm8	C	T	6: 27,363,752 (GRCm39)	V588M	probably benign	Het
H1f8	A	G	6: 115,926,911 (GRCm39)	T263A	probably benign	Het
Hoatz	T	A	9: 50,992,832 (GRCm39)		probably null	Het
Inhca	T	C	9: 103,149,831 (GRCm39)	Y242C	probably damaging	Het
Malrd1	T	A	2: 15,570,368 (GRCm39)		probably null	Het
Mxi1	G	A	19: 53,360,126 (GRCm39)	G283S	probably damaging	Het
Myh15	T	C	16: 48,997,366 (GRCm39)	V1728A	probably benign	Het
Nxph2	T	A	2: 23,290,071 (GRCm39)	V141D	probably damaging	Het
Or11l3	T	C	11: 58,515,994 (GRCm39)	E106G	unknown	Het
Or2t26	A	T	11: 49,039,483 (GRCm39)	Y133F	probably damaging	Het
Or4f6	A	T	2: 111,838,596 (GRCm39)	S312T	possibly damaging	Het
Or5b121	A	T	19: 13,507,892 (GRCm39)	N329I	probably damaging	Het
Or5d36	T	A	2: 87,901,753 (GRCm39)		probably null	Het
Or5h25	A	G	16: 58,930,121 (GRCm39)	V284A		Het
Or5w10	A	T	2: 87,375,753 (GRCm39)	M45K	probably damaging	Het
Or8c10	A	G	9: 38,279,142 (GRCm39)	N90S	possibly damaging	Het
Otof	T	A	5: 30,578,325 (GRCm39)	I108F	probably benign	Het
Pcdha4	A	T	18: 37,086,011 (GRCm39)	R65*	probably null	Het
Pde11a	T	C	2: 76,041,434 (GRCm39)	H412R	probably benign	Het
Peli3	C	T	19: 4,982,541 (GRCm39)	G375S	probably damaging	Het
Ppp6r3	A	G	19: 3,561,927 (GRCm39)		probably null	Het
Prcp	T	C	7: 92,559,518 (GRCm39)	V194A	possibly damaging	Het
Prkce	T	C	17: 86,476,370 (GRCm39)		probably null	Het
Prss23	A	T	7: 89,159,887 (GRCm39)	S61T	probably benign	Het
Ptprq	C	T	10: 107,535,469 (GRCm39)	R432H	probably damaging	Het
Rnase2a	T	A	14: 51,493,101 (GRCm39)	N88I	possibly damaging	Het
Rspry1	G	T	8: 95,359,780 (GRCm39)	L230F	probably damaging	Het
Slco1a8	A	G	6: 141,927,810 (GRCm39)	V548A	probably damaging	Het
Sorl1	A	G	9: 41,933,722 (GRCm39)	Y1083H	probably benign	Het
Tjp1	A	G	7: 64,986,386 (GRCm39)	S241P	probably damaging	Het
Tmed6	A	C	8: 107,792,164 (GRCm39)	L27R	probably damaging	Het
Tmem52	G	A	4: 155,553,788 (GRCm39)	C32Y	probably damaging	Het
Tmprss15	C	A	16: 78,750,834 (GRCm39)	G1022*	probably null	Het
Ttn	T	C	2: 76,730,345 (GRCm39)	S5085G	unknown	Het
Vmn2r37	C	T	7: 9,209,854 (GRCm39)	V553M	possibly damaging	Het
Wdr70	A	T	15: 8,123,210 (GRCm39)	M42K	probably benign	Het
Zfp735	T	A	11: 73,602,510 (GRCm39)	C485S	possibly damaging	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
R5383:Smpd2	UTSW	10	41,364,698 (GRCm39)	intron	probably benign
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
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'- AGCTCTACTGCTAAGATCAACC -3'
(R):5'- AGCGCTTGGGAGACTTTCTG -3'

Sequencing Primer
(F):5'- TCTACTGCTAAGATCAACCCCAGAAC -3'
(R):5'- AAAACTTTGATCTGGCTCTCCTGGAG -3'

Posted On

2021-07-15