Mutagenetix > Incidental Mutation

Incidental Mutation 'R6833:Smpd2'

534449

Institutional Source

Beutler Lab

Gene Symbol

Smpd2

Ensembl Gene

ENSMUSG00000019822

Gene Name

sphingomyelin phosphodiesterase 2, neutral

Synonyms

nSMase

MMRRC Submission

044942-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6833 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

41363168-41366410 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 41364442 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 160 (A160T)

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 damaging
Transcript: ENSMUST00000019965
AA Change: A160T

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000019965
Gene: ENSMUSG00000019822
AA Change: A160T

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

Meta Mutation Damage Score

0.3481

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.0%

Validation Efficiency

96% (54/56)

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
A830018L16Rik	T	A	1: 11,658,733 (GRCm39)	W215R	probably damaging	Het
Aco1	A	G	4: 40,164,747 (GRCm39)	K79R	probably benign	Het
Adam28	C	T	14: 68,855,576 (GRCm39)	A630T	probably benign	Het
Alpk2	T	C	18: 65,439,480 (GRCm39)	K1105E	probably benign	Het
Angptl1	A	T	1: 156,672,263 (GRCm39)	I30L	probably benign	Het
Astn1	A	T	1: 158,491,692 (GRCm39)	Q47L	probably benign	Het
Atf6b	T	C	17: 34,868,131 (GRCm39)	S135P	probably damaging	Het
Ccdc122	G	T	14: 77,326,371 (GRCm39)		probably benign	Het
Cers3	T	C	7: 66,429,419 (GRCm39)		probably null	Het
Dcaf10	T	C	4: 45,373,043 (GRCm39)	C95R	probably damaging	Het
Dcxr	A	G	11: 120,616,917 (GRCm39)	Y149H	probably damaging	Het
Dmxl1	A	T	18: 50,088,890 (GRCm39)	I2790F	probably damaging	Het
Dnhd1	T	A	7: 105,352,580 (GRCm39)	C2578S	probably benign	Het
Dnttip2	T	C	3: 122,070,452 (GRCm39)	S556P	probably damaging	Het
Efr3a	T	G	15: 65,714,535 (GRCm39)	V301G	probably damaging	Het
Eml5	A	T	12: 98,853,283 (GRCm39)	H105Q	probably damaging	Het
Enpp3	T	A	10: 24,685,768 (GRCm39)	H44L	probably damaging	Het
Fam120a	A	G	13: 49,087,517 (GRCm39)	V281A	probably damaging	Het
Fat3	C	T	9: 15,826,357 (GRCm39)	E4532K	possibly damaging	Het
Ferd3l	G	A	12: 33,978,537 (GRCm39)	V17I	probably damaging	Het
Glb1l	A	G	1: 75,178,397 (GRCm39)	V347A	possibly damaging	Het
Gm4846	A	T	1: 166,322,147 (GRCm39)	I140N	possibly damaging	Het
Gm9195	T	C	14: 72,671,856 (GRCm39)	T2586A	possibly damaging	Het
Hsd17b8	T	C	17: 34,246,191 (GRCm39)	S161G	probably damaging	Het
Hsp90ab1	T	C	17: 45,881,393 (GRCm39)	I250V	probably benign	Het
Il11ra1	A	G	4: 41,765,454 (GRCm39)	H183R	probably benign	Het
Lama3	G	A	18: 12,624,605 (GRCm39)	C1450Y	probably damaging	Het
Lgals7	G	A	7: 28,565,087 (GRCm39)	R75Q	probably damaging	Het
Lpcat3	A	G	6: 124,676,974 (GRCm39)	Y124C	probably damaging	Het
Lrrc8a	T	A	2: 30,145,659 (GRCm39)	S158T	possibly damaging	Het
Mcm3	A	T	1: 20,880,320 (GRCm39)	M504K	possibly damaging	Het
Mro	G	T	18: 73,997,003 (GRCm39)		probably benign	Het
Mybpc3	A	G	2: 90,955,773 (GRCm39)		probably null	Het
Myh14	T	A	7: 44,273,803 (GRCm39)	K1356*	probably null	Het
Myo5b	A	C	18: 74,903,396 (GRCm39)	Q1804P	probably benign	Het
Nol10	A	G	12: 17,402,728 (GRCm39)	I67V	probably benign	Het
Pam	T	A	1: 97,765,717 (GRCm39)	I771F	probably damaging	Het
Pcdhgb8	G	T	18: 37,895,142 (GRCm39)	A71S	probably benign	Het
Pmfbp1	T	C	8: 110,265,307 (GRCm39)		probably null	Het
Poc1b	C	T	10: 99,028,666 (GRCm39)	A336V	probably benign	Het
Poglut3	A	G	9: 53,303,308 (GRCm39)	I67V	possibly damaging	Het
Prap1	C	A	7: 139,674,995 (GRCm39)	A20E	possibly damaging	Het
Prox1	G	A	1: 189,892,975 (GRCm39)	A490V	probably damaging	Het
Prss39	G	T	1: 34,537,697 (GRCm39)	V54F	possibly damaging	Het
Sema3b	T	A	9: 107,480,515 (GRCm39)	E144V	probably benign	Het
Sft2d1	C	T	17: 8,537,707 (GRCm39)	T32I	possibly damaging	Het
Stard9	G	T	2: 120,531,740 (GRCm39)	V2666F	probably damaging	Het
Syt7	T	A	19: 10,421,508 (GRCm39)	M400K	probably damaging	Het
Thoc5	T	C	11: 4,869,804 (GRCm39)	L402P	probably damaging	Het
Tinf2	A	T	14: 55,919,037 (GRCm39)	M1K	probably null	Het
Ttc21a	A	G	9: 119,771,701 (GRCm39)	I167V	probably benign	Het
Vldlr	T	C	19: 27,217,974 (GRCm39)	L474P	probably damaging	Het
Xirp2	T	C	2: 67,340,294 (GRCm39)	V845A	probably benign	Het
Zdhhc7	A	T	8: 120,811,663 (GRCm39)	M180K	probably damaging	Het
Zfp735	G	A	11: 73,601,434 (GRCm39)	G126D	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
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'- CTGTCCACTCTTTCAGCAGG -3'
(R):5'- ATCAGAAGCTAGCATTGGGC -3'

Sequencing Primer
(F):5'- GGTGCATATTGAGGTCTCCACAC -3'
(R):5'- ATTGGGCAAGGTTCACCCATTC -3'

Posted On

2018-09-12