Mutagenetix > Incidental Mutation

Incidental Mutation 'R9275:Smpd2'

703233

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 #

R9275 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

41363168-41366410 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 41363685 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 289 (D289G)

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: D289G

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

SMART Domains

Protein: ENSMUSP00000019965
Gene: ENSMUSG00000019822
AA Change: D289G

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

SMART Domains

Protein: ENSMUSP00000115461
Gene: ENSMUSG00000019822

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

100% (66/66)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abr	A	G	11: 76,355,108 (GRCm39)	Y249H	probably damaging	Het
Afdn	T	A	17: 14,024,270 (GRCm39)	C59S	probably damaging	Het
Akap11	C	A	14: 78,751,149 (GRCm39)	V413F		Het
Ank3	T	C	10: 69,822,662 (GRCm39)	S444P	probably damaging	Het
Ankrd12	C	T	17: 66,344,599 (GRCm39)	E91K	possibly damaging	Het
Arhgap10	A	G	8: 78,137,665 (GRCm39)	S309P	probably damaging	Het
Arpc2	C	A	1: 74,276,041 (GRCm39)	F19L	probably benign	Het
Atp5f1a	C	T	18: 77,868,997 (GRCm39)	T457I	probably damaging	Het
Bsn	C	T	9: 107,988,819 (GRCm39)	R2311H	probably damaging	Het
C1ra	A	G	6: 124,494,383 (GRCm39)	T277A	probably benign	Het
Celsr3	C	G	9: 108,715,689 (GRCm39)	L2124V	probably benign	Het
Cenpv	T	C	11: 62,415,989 (GRCm39)	*253W	probably null	Het
Cfap54	A	T	10: 92,875,048 (GRCm39)	V479E	possibly damaging	Het
Clec1a	T	C	6: 129,428,564 (GRCm39)		probably benign	Het
Cmpk2	A	T	12: 26,519,568 (GRCm39)	Y73F	probably benign	Het
Cpne2	T	C	8: 95,281,643 (GRCm39)	I226T	possibly damaging	Het
Cyp2c67	C	T	19: 39,597,699 (GRCm39)	R433Q	probably damaging	Het
Dagla	A	G	19: 10,232,220 (GRCm39)	Y489H	probably damaging	Het
Dennd4a	C	A	9: 64,749,906 (GRCm39)	P166T	probably damaging	Het
Dnm2	C	T	9: 21,416,977 (GRCm39)	R837W	possibly damaging	Het
Enpp2	C	T	15: 54,713,484 (GRCm39)	R658Q	probably benign	Het
Gm10521	G	A	1: 171,724,030 (GRCm39)	V114I	unknown	Het
H2-T24	T	A	17: 36,328,276 (GRCm39)	E69V	probably damaging	Het
H6pd	T	A	4: 150,080,307 (GRCm39)	K179N	probably damaging	Het
Hsf2bp	C	T	17: 32,206,336 (GRCm39)	W265*	probably null	Het
Igfn1	C	A	1: 135,901,185 (GRCm39)	R431L	probably damaging	Het
Kcng2	T	C	18: 80,339,074 (GRCm39)	S405G	possibly damaging	Het
Leng9	T	C	7: 4,151,447 (GRCm39)	T410A	probably benign	Het
Lrp1b	T	C	2: 40,487,076 (GRCm39)	Y4557C		Het
Ltbp2	G	A	12: 84,837,864 (GRCm39)	P1192L	probably benign	Het
Mlkl	A	G	8: 112,043,055 (GRCm39)	V364A	probably benign	Het
Mns1	T	A	9: 72,356,507 (GRCm39)	F254Y	probably benign	Het
Naip1	T	A	13: 100,562,684 (GRCm39)	N827I	probably damaging	Het
Neb	C	T	2: 52,146,190 (GRCm39)	R2929H	probably damaging	Het
Or5m13	A	G	2: 85,749,046 (GRCm39)	Y259C	probably benign	Het
Or5v1b	T	A	17: 37,841,819 (GRCm39)	M317K	probably benign	Het
Pde10a	A	G	17: 9,200,488 (GRCm39)	*797W	probably null	Het
Pirb	T	G	7: 3,719,859 (GRCm39)	H429P	probably benign	Het
Plbd1	A	G	6: 136,594,286 (GRCm39)	L321P	probably damaging	Het
Pmfbp1	A	G	8: 110,262,471 (GRCm39)	I722V	probably benign	Het
Polr2b	A	G	5: 77,471,485 (GRCm39)	R274G	probably damaging	Het
Prune2	C	T	19: 17,101,144 (GRCm39)	T2216I	probably benign	Het
Psma3	A	T	12: 71,041,156 (GRCm39)	D252V	probably benign	Het
Ptpn1	C	T	2: 167,816,176 (GRCm39)	T230I	probably damaging	Het
Rhpn1	T	C	15: 75,585,120 (GRCm39)	V519A	possibly damaging	Het
Rnf213	T	C	11: 119,326,768 (GRCm39)	V1586A		Het
Rrp36	T	A	17: 46,983,306 (GRCm39)	K103*	probably null	Het
Ryr2	T	C	13: 11,897,976 (GRCm39)	T140A	probably benign	Het
Scn1a	T	A	2: 66,130,026 (GRCm39)	Y243F	probably damaging	Het
Sdk1	A	G	5: 141,941,953 (GRCm39)	T534A	possibly damaging	Het
Slc27a5	T	C	7: 12,731,640 (GRCm39)	D117G	probably damaging	Het
Slc2a1	A	T	4: 118,990,607 (GRCm39)	E246D	probably benign	Het
Spag6	A	C	2: 18,703,985 (GRCm39)	E11A	probably benign	Het
Stard3	G	A	11: 98,262,931 (GRCm39)		probably benign	Het
Tcf19	A	G	17: 35,825,899 (GRCm39)	V86A	probably damaging	Het
Tcstv7a	T	C	13: 120,289,993 (GRCm39)	S68G	possibly damaging	Het
Tigit	A	T	16: 43,479,833 (GRCm39)	M154K	probably benign	Het
Trim34a	T	A	7: 103,910,201 (GRCm39)	N334K	probably damaging	Het
Tsen15	T	C	1: 152,259,098 (GRCm39)	I87V	probably damaging	Het
Ttn	A	T	2: 76,738,218 (GRCm39)	M4153K	unknown	Het
Uchl3	A	T	14: 101,905,963 (GRCm39)		probably null	Het
Usp1	A	G	4: 98,819,578 (GRCm39)	K347E	probably damaging	Het
Vmn1r73	T	C	7: 11,490,479 (GRCm39)	M99T	probably benign	Het
Vmn2r20	A	G	6: 123,362,394 (GRCm39)	W797R	probably damaging	Het
Vwa7	A	G	17: 35,238,712 (GRCm39)	T267A	probably damaging	Het
Zpld2	A	G	4: 133,922,770 (GRCm39)	L521P	probably 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
R8869:Smpd2	UTSW	10	41,365,301 (GRCm39)	missense	probably benign
R9200:Smpd2	UTSW	10	41,363,561 (GRCm39)	missense	probably benign	0.03
R9621:Smpd2	UTSW	10	41,364,283 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- CATAGCCAGAGAATGCAGCC -3'
(R):5'- TAGAATCCTGTCGGCTGGTTC -3'

Sequencing Primer
(F):5'- AGCCCACCAGCGAGCTTTAG -3'
(R):5'- TCTCTGGGAGAATTTAAGCTTCTC -3'

Posted On

2022-03-25