Mutagenetix > Incidental Mutation

Incidental Mutation 'R1832:Smpd2'

204878

Institutional Source

Beutler Lab

Gene Symbol

Smpd2

Ensembl Gene

ENSMUSG00000019822

Gene Name

sphingomyelin phosphodiesterase 2, neutral

Synonyms

nSMase

MMRRC Submission

039859-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1832 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

41363168-41366410 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 41364232 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 189 (C189S)

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: C189S

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000019965
Gene: ENSMUSG00000019822
AA Change: C189S

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: ENSMUST00000132170

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138657

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147738

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125099

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143470

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147367

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141542

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126833

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134010

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000215608

Meta Mutation Damage Score

0.0916

Coding Region Coverage

1x: 97.4%
3x: 96.7%
10x: 94.6%
20x: 90.7%

Validation Efficiency

100% (82/82)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700003H04Rik	T	A	3: 124,350,509 (GRCm39)	D143V	unknown	Het
Abca8a	A	T	11: 109,962,277 (GRCm39)	N525K	probably damaging	Het
Abhd12	T	A	2: 150,690,338 (GRCm39)	D119V	probably damaging	Het
Adamts20	A	T	15: 94,184,225 (GRCm39)	M1526K	probably benign	Het
Ankdd1a	A	T	9: 65,411,771 (GRCm39)		probably null	Het
Ankrd1	C	T	19: 36,092,378 (GRCm39)	C283Y	possibly damaging	Het
Arfgef1	G	C	1: 10,275,115 (GRCm39)	I312M	probably benign	Het
Bhlhe22	G	A	3: 18,109,139 (GRCm39)	C63Y	probably damaging	Het
Bmp8a	A	T	4: 123,218,885 (GRCm39)		probably benign	Het
Ccdc148	A	T	2: 58,891,911 (GRCm39)	S235T	probably damaging	Het
Ccdc88b	G	A	19: 6,830,900 (GRCm39)	Q681*	probably null	Het
Cep104	T	A	4: 154,087,003 (GRCm39)	V842E	probably benign	Het
Chac2	T	C	11: 30,927,568 (GRCm39)	N117S	probably benign	Het
Cimap3	C	T	3: 105,921,912 (GRCm39)	E4K	possibly damaging	Het
Cldn8	T	A	16: 88,359,746 (GRCm39)	I60F	probably benign	Het
Col16a1	G	A	4: 129,970,850 (GRCm39)		probably null	Het
Col4a1	A	G	8: 11,264,644 (GRCm39)		probably benign	Het
Cyp2a4	G	T	7: 26,011,635 (GRCm39)	E285D	probably damaging	Het
Cyp4a31	G	A	4: 115,426,928 (GRCm39)	G176D	probably benign	Het
Dmxl2	A	C	9: 54,368,233 (GRCm39)	Y246D	probably damaging	Het
Dync1h1	A	G	12: 110,580,493 (GRCm39)	K118R	probably damaging	Het
Dync2i1	T	A	12: 116,171,363 (GRCm39)	S958C	probably damaging	Het
Eif3h	T	C	15: 51,728,832 (GRCm39)	T8A	possibly damaging	Het
Fbh1	G	T	2: 11,772,211 (GRCm39)	L157I	probably benign	Het
Fbxo40	C	A	16: 36,789,218 (GRCm39)	G631*	probably null	Het
Gabrb1	T	A	5: 72,279,281 (GRCm39)		probably null	Het
Galc	A	G	12: 98,200,499 (GRCm39)		probably null	Het
Garin2	G	A	12: 78,762,280 (GRCm39)		probably benign	Het
H2-Q7	C	A	17: 35,658,675 (GRCm39)	S104R	probably benign	Het
Igkv13-54-1	A	T	6: 69,594,277 (GRCm39)	M31L	probably benign	Het
Lamc2	C	T	1: 153,041,933 (GRCm39)	R67Q	possibly damaging	Het
Lcn10	A	G	2: 25,575,151 (GRCm39)	D173G	probably damaging	Het
Llgl2	G	T	11: 115,741,926 (GRCm39)	R656L	probably damaging	Het
Lonrf2	G	A	1: 38,852,357 (GRCm39)	P165S	probably benign	Het
Lrrc66	G	A	5: 73,764,769 (GRCm39)	S758L	possibly damaging	Het
Ly6d	T	C	15: 74,634,615 (GRCm39)	K46E	probably damaging	Het
Map3k5	A	G	10: 19,975,306 (GRCm39)	N88D	probably damaging	Het
Mertk	A	T	2: 128,604,132 (GRCm39)	E422V	probably benign	Het
Mixl1	A	G	1: 180,522,296 (GRCm39)	V195A	probably benign	Het
Nmnat3	T	C	9: 98,281,521 (GRCm39)	V41A	probably damaging	Het
Or1r1	A	T	11: 73,875,319 (GRCm39)	N38K	probably damaging	Het
Or2a7	A	G	6: 43,151,834 (GRCm39)	R305G	probably benign	Het
Or7g34	A	G	9: 19,478,492 (GRCm39)	Y63H	possibly damaging	Het
Pappa2	T	A	1: 158,684,886 (GRCm39)	E751V	probably damaging	Het
Pcsk2	A	G	2: 143,635,189 (GRCm39)	S355G	probably damaging	Het
Pdzd2	A	G	15: 12,390,134 (GRCm39)	V821A	probably damaging	Het
Plxna4	A	C	6: 32,174,761 (GRCm39)	D1109E	probably benign	Het
Ppard	A	G	17: 28,516,084 (GRCm39)	M103V	probably benign	Het
Pramel51	T	C	12: 88,145,218 (GRCm39)	E44G	possibly damaging	Het
Ralgapa1	T	C	12: 55,804,752 (GRCm39)	T515A	probably benign	Het
Rin2	A	G	2: 145,703,091 (GRCm39)	I596V	possibly damaging	Het
Rnls	A	G	19: 33,145,895 (GRCm39)	S75P	possibly damaging	Het
Rsph10b	A	T	5: 143,903,997 (GRCm39)	Y236F	possibly damaging	Het
Runx1t1	C	T	4: 13,835,628 (GRCm39)		probably benign	Het
Sardh	A	G	2: 27,125,581 (GRCm39)	V311A	possibly damaging	Het
Sbno2	G	T	10: 79,896,439 (GRCm39)	Y889*	probably null	Het
Sclt1	A	G	3: 41,681,546 (GRCm39)	V91A	probably damaging	Het
Sema4g	T	A	19: 44,987,456 (GRCm39)	V534E	probably benign	Het
Shoc1	T	G	4: 59,066,441 (GRCm39)	I768L	probably benign	Het
Slc10a1	G	A	12: 81,000,446 (GRCm39)	S351F	probably benign	Het
Slc19a3	A	T	1: 83,000,468 (GRCm39)	V183E	probably damaging	Het
Slc25a12	A	G	2: 71,164,054 (GRCm39)	Y74H	possibly damaging	Het
Slc6a19	T	A	13: 73,841,069 (GRCm39)	I114L	probably benign	Het
Spon1	T	A	7: 113,616,018 (GRCm39)	V295D	probably benign	Het
Tet3	A	G	6: 83,380,627 (GRCm39)	S514P	probably benign	Het
Tnk1	T	C	11: 69,747,754 (GRCm39)	I49M	probably damaging	Het
Trim80	A	G	11: 115,337,619 (GRCm39)	T431A	probably benign	Het
Vgf	A	T	5: 137,060,153 (GRCm39)	Q105L	possibly damaging	Het
Vmn1r37	G	T	6: 66,708,780 (GRCm39)	L135F	probably benign	Het
Vps37d	C	T	5: 135,102,594 (GRCm39)	A128T	possibly damaging	Het
Wwp1	T	C	4: 19,650,197 (GRCm39)	D323G	probably benign	Het
Zfp456	T	A	13: 67,515,482 (GRCm39)	I75L	probably benign	Het
Zfp990	A	G	4: 145,264,780 (GRCm39)	I593V	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
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
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'- TAATCAATCCGGATACCAGACG -3'
(R):5'- GTTCATCCAGTGTGTGAGCC -3'

Sequencing Primer
(F):5'- ACGTAGCAGTTCTTGGGTAC -3'
(R):5'- CAGTGTGTGAGCCTGGGC -3'

Posted On

2014-06-23