Mutagenetix > Incidental Mutation

Incidental Mutation 'R1758:Smpd4'

195128

Institutional Source

Beutler Lab

Gene Symbol

Smpd4

Ensembl Gene

ENSMUSG00000005899

Gene Name

sphingomyelin phosphodiesterase 4

Synonyms

4122402O22Rik, neutral membrane (neutral sphingomyelinase-3)

MMRRC Submission

039790-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.098) question?

Stock #

R1758 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

17437218-17462692 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 17443872 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 112 (S112P)

Ref Sequence

ENSEMBL: ENSMUSP00000130990 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000165363] [ENSMUST00000168101] [ENSMUST00000171435] [ENSMUST00000170366] [ENSMUST00000231257] [ENSMUST00000231436] [ENSMUST00000231311] [ENSMUST00000231887] [ENSMUST00000231722] [ENSMUST00000231627] [ENSMUST00000231792] [ENSMUST00000232116] [ENSMUST00000232043] [ENSMUST00000232271] [ENSMUST00000232021] [ENSMUST00000232442]

AlphaFold

Q6ZPR5

Predicted Effect

possibly damaging
Transcript: ENSMUST00000006053
AA Change: S112P

PolyPhen 2 Score 0.614 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: S112P

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	768	N/A	PFAM
transmembrane domain	769	791	N/A	INTRINSIC
transmembrane domain	798	815	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000087486

Predicted Effect

possibly damaging
Transcript: ENSMUST00000090159
AA Change: S112P

PolyPhen 2 Score 0.614 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: S112P

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	288	7.4e-177	PFAM
Pfam:mit_SMPDase	287	752	9.4e-259	PFAM
transmembrane domain	753	775	N/A	INTRINSIC
transmembrane domain	782	799	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000163476
AA Change: S112P

PolyPhen 2 Score 0.614 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: S112P

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	289	6.2e-177	PFAM
Pfam:mit_SMPDase	285	739	9.8e-266	PFAM
transmembrane domain	740	762	N/A	INTRINSIC
transmembrane domain	769	786	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000165363
AA Change: S112P

PolyPhen 2 Score 0.614 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: S112P

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	289	6.2e-177	PFAM
Pfam:mit_SMPDase	285	738	4.1e-262	PFAM
transmembrane domain	739	761	N/A	INTRINSIC
transmembrane domain	768	785	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166091

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166322

Predicted Effect

possibly damaging
Transcript: ENSMUST00000168101
AA Change: S83P

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000129995
Gene: ENSMUSG00000005899
AA Change: S83P

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	125	6.8e-70	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000171435
AA Change: S120P

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000131560
Gene: ENSMUSG00000005899
AA Change: S120P

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	129	4.4e-69	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000170366
AA Change: S112P

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000130990
Gene: ENSMUSG00000005899
AA Change: S112P

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	288	7.1e-177	PFAM
Pfam:mit_SMPDase	286	643	1.8e-214	PFAM
Pfam:mit_SMPDase	642	696	8.6e-18	PFAM
transmembrane domain	697	719	N/A	INTRINSIC
transmembrane domain	726	743	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170401

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167362

Predicted Effect

possibly damaging
Transcript: ENSMUST00000231257
AA Change: S83P

PolyPhen 2 Score 0.852 (Sensitivity: 0.83; Specificity: 0.93)

Predicted Effect

probably damaging
Transcript: ENSMUST00000231436
AA Change: S112P

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000231311
AA Change: S120P

PolyPhen 2 Score 0.852 (Sensitivity: 0.83; Specificity: 0.93)

Predicted Effect

probably benign
Transcript: ENSMUST00000231887

Predicted Effect

probably benign
Transcript: ENSMUST00000231722

Predicted Effect

probably benign
Transcript: ENSMUST00000231627

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231736

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231949

Predicted Effect

probably benign
Transcript: ENSMUST00000231792

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232468

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232578

Predicted Effect

probably benign
Transcript: ENSMUST00000232116

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232487

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232417

Predicted Effect

probably benign
Transcript: ENSMUST00000232043

Predicted Effect

probably benign
Transcript: ENSMUST00000232271

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232185

Predicted Effect

probably benign
Transcript: ENSMUST00000232021

Predicted Effect

probably benign
Transcript: ENSMUST00000232442

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.6%
20x: 93.2%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Sphingomyelinases (EC 3.1.4.12), such as SMPD4, catalyze the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (Krut et al., 2006 [PubMed 16517606]).[supplied by OMIM, Mar 2008]

Allele List at MGI

Other mutations in this stock

Total: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700029H14Rik	T	C	8: 13,612,237 (GRCm39)	R38G	possibly damaging	Het
4930590J08Rik	T	C	6: 91,892,203 (GRCm39)	V155A	possibly damaging	Het
Adgb	A	G	10: 10,302,349 (GRCm39)	S406P	probably damaging	Het
Adgrb2	C	A	4: 129,905,668 (GRCm39)	T893N	probably damaging	Het
Adgrf5	T	C	17: 43,735,484 (GRCm39)		probably null	Het
Alms1	T	A	6: 85,605,487 (GRCm39)	I2379N	probably damaging	Het
Arap3	C	T	18: 38,122,965 (GRCm39)	V512I	probably benign	Het
Atf4	C	T	15: 80,141,414 (GRCm39)	T268I	probably benign	Het
Cblif	G	A	19: 11,735,179 (GRCm39)	M266I	probably damaging	Het
Ccdc154	T	C	17: 25,382,156 (GRCm39)	L25P	probably damaging	Het
Ccdc9	G	A	7: 16,010,161 (GRCm39)	S381F	probably damaging	Het
Cdk17	C	T	10: 93,044,112 (GRCm39)	T17M	probably damaging	Het
Cep128	T	C	12: 91,314,352 (GRCm39)	N142S	probably benign	Het
Cep78	A	G	19: 15,936,900 (GRCm39)	I602T	probably damaging	Het
Clasp1	C	T	1: 118,475,755 (GRCm39)	T935I	probably damaging	Het
Cnr1	T	C	4: 33,945,000 (GRCm39)	S463P	probably damaging	Het
Cntnap1	T	A	11: 101,075,449 (GRCm39)	W876R	probably damaging	Het
Cntnap5c	A	G	17: 58,349,545 (GRCm39)	D286G	probably damaging	Het
Copa	C	T	1: 171,931,711 (GRCm39)	R321C	probably damaging	Het
Cspg4b	A	G	13: 113,505,266 (GRCm39)	T2132A	possibly damaging	Het
Ctla2a	T	G	13: 61,083,256 (GRCm39)	E98A	probably damaging	Het
Cux1	A	T	5: 136,421,176 (GRCm39)	D183E	probably damaging	Het
Cxcl15	A	C	5: 90,949,323 (GRCm39)	T163P	unknown	Het
Ddias	T	C	7: 92,508,571 (GRCm39)	N448S	probably benign	Het
Dhx8	T	C	11: 101,657,564 (GRCm39)	F1152S	probably damaging	Het
Dnah12	C	A	14: 26,488,071 (GRCm39)	Q992K	probably benign	Het
Eno3	G	T	11: 70,552,251 (GRCm39)	W301L	possibly damaging	Het
Faap100	A	T	11: 120,268,059 (GRCm39)	V238E	probably damaging	Het
Fgf4	A	G	7: 144,416,049 (GRCm39)	S137G	probably benign	Het
Fhod3	A	C	18: 25,253,367 (GRCm39)	D1439A	possibly damaging	Het
Frem2	A	G	3: 53,560,778 (GRCm39)	L1243P	probably damaging	Het
Gkn3	T	G	6: 87,365,817 (GRCm39)	M1L	probably benign	Het
Gm10250	T	C	15: 5,150,509 (GRCm39)		probably benign	Het
Gm12185	T	C	11: 48,798,859 (GRCm39)	T545A	possibly damaging	Het
Gm14226	T	A	2: 154,867,378 (GRCm39)	L445H	probably damaging	Het
Gm3404	A	T	5: 146,463,036 (GRCm39)	M73L	probably benign	Het
Gm973	G	T	1: 59,673,169 (GRCm39)	R976S	unknown	Het
Gpr146	A	T	5: 139,379,137 (GRCm39)	H313L	probably benign	Het
Gys2	T	A	6: 142,418,432 (GRCm39)	E32D	probably damaging	Het
Igsf10	G	A	3: 59,236,617 (GRCm39)	T1188I	probably benign	Het
Igsf9b	A	T	9: 27,245,548 (GRCm39)	T1172S	possibly damaging	Het
Itga8	T	A	2: 12,270,144 (GRCm39)	N114I	possibly damaging	Het
Itsn2	T	A	12: 4,708,160 (GRCm39)	V795E	possibly damaging	Het
Kdm1b	T	A	13: 47,214,244 (GRCm39)	S197T	probably benign	Het
Kif5c	G	A	2: 49,613,145 (GRCm39)	R161Q	probably benign	Het
Krt33b	T	C	11: 99,916,361 (GRCm39)	Y232C	probably damaging	Het
Lonrf2	G	A	1: 38,852,357 (GRCm39)	P165S	probably benign	Het
Lrp1	A	T	10: 127,424,453 (GRCm39)	N744K	possibly damaging	Het
Mcm10	C	A	2: 5,008,861 (GRCm39)	L369F	probably damaging	Het
Muc5ac	T	A	7: 141,355,268 (GRCm39)	I1018N	possibly damaging	Het
Myom2	T	C	8: 15,115,795 (GRCm39)	L70P	probably benign	Het
Myt1l	T	A	12: 29,877,241 (GRCm39)	N297K	unknown	Het
Ncr1	C	T	7: 4,343,807 (GRCm39)	T98I	probably benign	Het
Nek3	T	C	8: 22,650,278 (GRCm39)	E78G	probably damaging	Het
Nfatc3	T	A	8: 106,825,768 (GRCm39)	N606K	probably damaging	Het
Nup107	T	G	10: 117,597,248 (GRCm39)	D669A	probably damaging	Het
Or10ag52	A	T	2: 87,043,758 (GRCm39)	Q174L	probably benign	Het
Or10c1	A	T	17: 37,522,204 (GRCm39)	I180N	possibly damaging	Het
Or4c3	T	C	2: 89,851,673 (GRCm39)	T246A	probably benign	Het
Or8b55	A	T	9: 38,726,871 (GRCm39)	H24L	probably benign	Het
Pcnx1	T	C	12: 82,030,258 (GRCm39)	V1711A	probably benign	Het
Pik3c3	A	G	18: 30,410,063 (GRCm39)	D99G	probably damaging	Het
Pinx1	C	A	14: 64,157,024 (GRCm39)	T317K	probably benign	Het
Ppargc1b	G	T	18: 61,431,857 (GRCm39)		probably null	Het
Pradc1	T	A	6: 85,424,203 (GRCm39)	I119F	possibly damaging	Het
Psat1	G	T	19: 15,892,243 (GRCm39)	T242K	probably damaging	Het
Psma6	G	A	12: 55,454,317 (GRCm39)	C28Y	probably damaging	Het
Pyurf	A	T	6: 57,668,817 (GRCm39)	C58*	probably null	Het
Rab3gap2	C	A	1: 185,016,081 (GRCm39)	A1331E	probably benign	Het
Rnase4	T	C	14: 51,342,722 (GRCm39)	*149Q	probably null	Het
Ruvbl2	T	C	7: 45,074,586 (GRCm39)	K184R	probably benign	Het
Scn7a	T	G	2: 66,510,527 (GRCm39)	M1292L	probably benign	Het
Scn7a	A	T	2: 66,531,231 (GRCm39)	Y549N	probably damaging	Het
Selp	A	G	1: 163,959,854 (GRCm39)	D370G	possibly damaging	Het
Slc22a15	G	A	3: 101,767,769 (GRCm39)	Q386*	probably null	Het
Slc22a29	A	G	19: 8,195,126 (GRCm39)		probably null	Het
Slc26a7	A	C	4: 14,548,491 (GRCm39)	I266S	possibly damaging	Het
Snx33	A	G	9: 56,833,982 (GRCm39)	I29T	probably benign	Het
Spen	G	A	4: 141,203,686 (GRCm39)	P1647L	unknown	Het
Strip2	T	C	6: 29,941,940 (GRCm39)		probably null	Het
Swsap1	C	T	9: 21,867,280 (GRCm39)	R75*	probably null	Het
Tesl1	A	G	X: 23,772,990 (GRCm39)	I164V	probably benign	Het
Tmem210	C	T	2: 25,178,435 (GRCm39)	T32I	probably damaging	Het
Tnn	C	T	1: 159,975,154 (GRCm39)	R91H	possibly damaging	Het
Tnni1	G	A	1: 135,736,420 (GRCm39)	R94H	probably damaging	Het
Tnrc6c	T	A	11: 117,651,556 (GRCm39)	V1693D	probably benign	Het
Trip4	G	A	9: 65,782,259 (GRCm39)	Q158*	probably null	Het
Ttc39b	T	C	4: 83,155,586 (GRCm39)	E474G	probably damaging	Het
Usp50	C	A	2: 126,617,782 (GRCm39)	C221F	probably damaging	Het
Vmn1r171	T	C	7: 23,331,781 (GRCm39)	I2T	probably benign	Het
Wdr62	T	A	7: 29,967,328 (GRCm39)	I309F	probably damaging	Het
Xdh	A	T	17: 74,217,204 (GRCm39)	V688E	probably damaging	Het
Zfyve26	A	G	12: 79,285,718 (GRCm39)	L2353P	probably damaging	Het
Zgpat	C	A	2: 181,020,633 (GRCm39)	R269S	probably damaging	Het

Other mutations in Smpd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00944:Smpd4	APN	16	17,460,621 (GRCm39)	missense	probably benign	0.04
IGL01461:Smpd4	APN	16	17,439,370 (GRCm39)	missense	probably damaging	1.00
IGL02051:Smpd4	APN	16	17,444,382 (GRCm39)	missense	probably damaging	1.00
IGL02492:Smpd4	APN	16	17,457,215 (GRCm39)	missense	probably damaging	1.00
IGL03181:Smpd4	APN	16	17,443,671 (GRCm39)	nonsense	probably null
Victim	UTSW	16	17,458,835 (GRCm39)	missense	probably damaging	1.00
weakling	UTSW	16	17,456,350 (GRCm39)	intron	probably benign
G1citation:Smpd4	UTSW	16	17,458,097 (GRCm39)	missense	probably damaging	1.00
R0197:Smpd4	UTSW	16	17,459,461 (GRCm39)	critical splice donor site	probably null
R0549:Smpd4	UTSW	16	17,457,176 (GRCm39)	missense	probably benign	0.15
R0789:Smpd4	UTSW	16	17,443,690 (GRCm39)	missense	probably benign	0.14
R1077:Smpd4	UTSW	16	17,441,833 (GRCm39)	missense	probably damaging	1.00
R1120:Smpd4	UTSW	16	17,456,350 (GRCm39)	intron	probably benign
R1716:Smpd4	UTSW	16	17,460,365 (GRCm39)	missense	probably damaging	1.00
R1758:Smpd4	UTSW	16	17,458,744 (GRCm39)	missense	probably damaging	1.00
R1838:Smpd4	UTSW	16	17,460,166 (GRCm39)	splice site	probably null
R2115:Smpd4	UTSW	16	17,444,729 (GRCm39)	missense	probably benign	0.33
R2849:Smpd4	UTSW	16	17,460,076 (GRCm39)	missense	probably damaging	1.00
R4654:Smpd4	UTSW	16	17,459,992 (GRCm39)	intron	probably benign
R6157:Smpd4	UTSW	16	17,458,930 (GRCm39)	splice site	probably null
R6190:Smpd4	UTSW	16	17,449,877 (GRCm39)	missense	probably damaging	1.00
R6822:Smpd4	UTSW	16	17,458,097 (GRCm39)	missense	probably damaging	1.00
R7062:Smpd4	UTSW	16	17,458,835 (GRCm39)	missense	probably damaging	1.00
R7305:Smpd4	UTSW	16	17,459,647 (GRCm39)	missense	probably damaging	0.99
R7759:Smpd4	UTSW	16	17,456,497 (GRCm39)	missense	probably damaging	1.00
R7853:Smpd4	UTSW	16	17,460,605 (GRCm39)	missense	probably damaging	1.00
R8187:Smpd4	UTSW	16	17,446,999 (GRCm39)	missense	probably damaging	1.00
R8303:Smpd4	UTSW	16	17,457,195 (GRCm39)	missense	probably damaging	1.00
R8518:Smpd4	UTSW	16	17,458,884 (GRCm39)	missense	possibly damaging	0.89
R8735:Smpd4	UTSW	16	17,453,410 (GRCm39)	missense	possibly damaging	0.92
R9075:Smpd4	UTSW	16	17,457,849 (GRCm39)	missense	unknown
R9439:Smpd4	UTSW	16	17,459,451 (GRCm39)	missense	probably benign
Z1176:Smpd4	UTSW	16	17,437,450 (GRCm39)	intron	probably benign
Z1177:Smpd4	UTSW	16	17,439,305 (GRCm39)	critical splice acceptor site	probably benign

Predicted Primers

PCR Primer
(F):5'- TGTGGAGTACAGCACAGCGATG -3'
(R):5'- CTGAGTGTCACACTTCAACCTGCC -3'

Sequencing Primer
(F):5'- AAGGGCTGAGTACTTCCTTG -3'
(R):5'- AACCTGCCCTGAAGGTCTG -3'

Posted On

2014-05-23