Mutagenetix > Incidental Mutation

Incidental Mutation 'R1838:Smpd4'

205545

Institutional Source

Beutler Lab

Gene Symbol

Smpd4

Ensembl Gene

ENSMUSG00000005899

Gene Name

sphingomyelin phosphodiesterase 4

Synonyms

4122402O22Rik, neutral membrane (neutral sphingomyelinase-3)

MMRRC Submission

039865-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.111) question?

Stock #

R1838 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

17619354-17644828 bp(+) (GRCm38)

Type of Mutation

splice site (5 bp from exon)

DNA Base Change (assembly)

G to A at 17642302 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000156215 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000056962] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000163997] [ENSMUST00000163997] [ENSMUST00000165363] [ENSMUST00000170117] [ENSMUST00000170273] [ENSMUST00000170273] [ENSMUST00000170996] [ENSMUST00000170996] [ENSMUST00000232116] [ENSMUST00000231627] [ENSMUST00000232271] [ENSMUST00000231722] [ENSMUST00000232021] [ENSMUST00000182117] [ENSMUST00000231436] [ENSMUST00000231792] [ENSMUST00000182344] [ENSMUST00000182368]

AlphaFold

Q6ZPR5

Predicted Effect

probably null
Transcript: ENSMUST00000006053

SMART Domains

Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899

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

probably benign
Transcript: ENSMUST00000056962

SMART Domains

Protein: ENSMUSP00000049541
Gene: ENSMUSG00000041617

Domain	Start	End	E-Value	Type
low complexity region	12	34	N/A	INTRINSIC
Pfam:CCDC92	50	105	4.1e-24	PFAM
low complexity region	154	164	N/A	INTRINSIC
Pfam:CCDC74_C	209	326	1.4e-49	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000090159

SMART Domains

Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899

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

probably null
Transcript: ENSMUST00000163476

SMART Domains

Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899

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

probably null
Transcript: ENSMUST00000163997

SMART Domains

Protein: ENSMUSP00000128595
Gene: ENSMUSG00000005899

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	43	2.1e-17	PFAM
Pfam:mit_SMPDase	42	68	2.5e-13	PFAM
Pfam:mit_SMPDase	65	518	4.9e-266	PFAM
transmembrane domain	519	541	N/A	INTRINSIC
transmembrane domain	548	565	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000163997

SMART Domains

Protein: ENSMUSP00000128595
Gene: ENSMUSG00000005899

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	43	2.1e-17	PFAM
Pfam:mit_SMPDase	42	68	2.5e-13	PFAM
Pfam:mit_SMPDase	65	518	4.9e-266	PFAM
transmembrane domain	519	541	N/A	INTRINSIC
transmembrane domain	548	565	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164292

Predicted Effect

probably null
Transcript: ENSMUST00000165363

SMART Domains

Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899

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: ENSMUST00000167362

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167592

Predicted Effect

SMART Domains

Protein: ENSMUSP00000132279
Gene: ENSMUSG00000005899

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	46	2.1e-19	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000170273

SMART Domains

Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	43	2.6e-17	PFAM
Pfam:mit_SMPDase	41	215	4.1e-103	PFAM
Pfam:mit_SMPDase	214	666	1.3e-265	PFAM
transmembrane domain	667	689	N/A	INTRINSIC
transmembrane domain	696	713	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000170273

SMART Domains

Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	43	2.6e-17	PFAM
Pfam:mit_SMPDase	41	215	4.1e-103	PFAM
Pfam:mit_SMPDase	214	666	1.3e-265	PFAM
transmembrane domain	667	689	N/A	INTRINSIC
transmembrane domain	696	713	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000170996

SMART Domains

Protein: ENSMUSP00000129074
Gene: ENSMUSG00000005899

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	26	444	4.4e-234	PFAM
transmembrane domain	445	467	N/A	INTRINSIC
transmembrane domain	474	491	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000170996

SMART Domains

Protein: ENSMUSP00000129074
Gene: ENSMUSG00000005899

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	26	444	4.4e-234	PFAM
transmembrane domain	445	467	N/A	INTRINSIC
transmembrane domain	474	491	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170401

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000182526

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000182822

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183101

Predicted Effect

probably benign
Transcript: ENSMUST00000182976

Predicted Effect

probably benign
Transcript: ENSMUST00000232116

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232270

Predicted Effect

probably benign
Transcript: ENSMUST00000231627

Predicted Effect

probably null
Transcript: ENSMUST00000232271

Predicted Effect

probably benign
Transcript: ENSMUST00000231722

Predicted Effect

probably null
Transcript: ENSMUST00000232021

Predicted Effect

probably benign
Transcript: ENSMUST00000182117

SMART Domains

Protein: ENSMUSP00000138657
Gene: ENSMUSG00000041617

Domain	Start	End	E-Value	Type
low complexity region	1	21	N/A	INTRINSIC
Pfam:CCDC92	36	97	2e-26	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232185

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231378

Predicted Effect

probably benign
Transcript: ENSMUST00000231436

Predicted Effect

probably null
Transcript: ENSMUST00000231792

Predicted Effect

probably benign
Transcript: ENSMUST00000182344

SMART Domains

Protein: ENSMUSP00000138131
Gene: ENSMUSG00000041617

Domain	Start	End	E-Value	Type
Pfam:CCDC92	18	79	1.4e-26	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000182368

SMART Domains

Protein: ENSMUSP00000138262
Gene: ENSMUSG00000041617

Domain	Start	End	E-Value	Type
low complexity region	12	34	N/A	INTRINSIC
Pfam:CCDC92	49	110	2.9e-26	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000182671

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232468

Predicted Effect

probably benign
Transcript: ENSMUST00000183279

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232417

Coding Region Coverage

1x: 97.4%
3x: 96.9%
10x: 95.2%
20x: 92.4%

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630073D07Rik	T	C	6: 132,626,727	D22G	unknown	Het
Abca4	G	A	3: 122,128,305	R1170K	probably benign	Het
Adam28	T	C	14: 68,639,210	N197S	possibly damaging	Het
Adamtsl3	G	T	7: 82,493,373	R267L	probably damaging	Het
Adgrb2	A	T	4: 130,010,231	T717S	probably benign	Het
Adgrb3	A	G	1: 25,084,270	S1417P	probably damaging	Het
Afg3l2	A	T	18: 67,414,172	V561D	probably damaging	Het
Atp13a2	T	A	4: 140,994,332	Y244*	probably null	Het
BB014433	C	G	8: 15,042,629	V75L	unknown	Het
Btnl6	T	A	17: 34,515,542	D82V	probably damaging	Het
Ccdc178	A	G	18: 22,067,638	Y421H	probably damaging	Het
Cdc123	A	T	2: 5,794,891		probably null	Het
Cdhr5	C	T	7: 141,272,603	V367I	possibly damaging	Het
Celsr3	A	G	9: 108,829,906	H1196R	probably benign	Het
Chd8	T	C	14: 52,204,883	S2077G	probably benign	Het
Col6a5	G	A	9: 105,864,833	H2296Y	probably benign	Het
Ctnna2	T	C	6: 77,845,542	D26G	probably damaging	Het
Ctr9	G	T	7: 111,052,303	R910L	possibly damaging	Het
Cyp2t4	G	T	7: 27,158,416	R455L	possibly damaging	Het
Cyp3a13	A	T	5: 137,911,632		probably null	Het
Dennd3	T	C	15: 73,565,100	S1059P	probably damaging	Het
Dennd4c	A	G	4: 86,825,178	T1135A	probably benign	Het
Dnah7b	T	C	1: 46,116,177	V295A	probably benign	Het
Dnah7b	C	A	1: 46,277,105	T3126K	probably damaging	Het
Ehbp1l1	C	T	19: 5,717,691	E1195K	probably benign	Het
Exoc6b	T	A	6: 84,853,678	I447L	probably benign	Het
Glt1d1	G	A	5: 127,678,129	V202I	probably benign	Het
Grk1	T	C	8: 13,416,155	V533A	possibly damaging	Het
Gsdma3	C	T	11: 98,629,858	A105V	probably benign	Het
Gzma	T	A	13: 113,095,984	I131F	probably damaging	Het
Helq	A	T	5: 100,771,879	L35*	probably null	Het
Hnrnpll	T	C	17: 80,038,623	N403S	probably damaging	Het
Hsf5	A	G	11: 87,636,055	K518E	probably benign	Het
Ighe	T	A	12: 113,271,850	H258L	unknown	Het
Il6ra	T	C	3: 89,890,272	D96G	probably benign	Het
Ints13	C	T	6: 146,566,611	A129T	possibly damaging	Het
Ipo7	T	A	7: 110,042,109	H345Q	probably damaging	Het
Kcna2	A	T	3: 107,104,512	E136D	probably benign	Het
Kif5a	G	A	10: 127,236,815	Q702*	probably null	Het
Klhdc7a	G	T	4: 139,967,070	P189T	probably benign	Het
Krtap4-9	A	G	11: 99,785,396		probably benign	Het
Lamc3	T	C	2: 31,925,582	S1097P	possibly damaging	Het
Ldlrad2	A	T	4: 137,572,170	N114K	probably benign	Het
Lrfn1	A	T	7: 28,459,768	I371L	probably damaging	Het
Lrwd1	A	G	5: 136,132,388	V240A	probably benign	Het
Lypd1	A	T	1: 125,873,371		probably benign	Het
Magi2	A	T	5: 20,465,827	T163S	probably damaging	Het
Man2c1	A	G	9: 57,137,337	N354S	probably benign	Het
Map3k13	T	C	16: 21,914,189	Y514H	possibly damaging	Het
Med15	T	C	16: 17,653,562	D577G	probably benign	Het
Mroh4	A	T	15: 74,616,113	M320K	probably benign	Het
Ms4a10	T	A	19: 10,964,047	D186V	possibly damaging	Het
Myh7	T	C	14: 54,973,180	N1725S	possibly damaging	Het
Myo5c	A	T	9: 75,273,553	R741S	probably damaging	Het
Naip6	T	C	13: 100,316,136	D139G	probably damaging	Het
Nat6	G	A	9: 107,583,017	R37H	possibly damaging	Het
Olfr1252	A	T	2: 89,721,709	M134K	probably damaging	Het
Olfr1370	A	T	13: 21,072,425	L292*	probably null	Het
Olfr229	A	T	9: 39,909,841	I13F	possibly damaging	Het
Olfr982	A	T	9: 40,074,309	M5L	probably benign	Het
Pcdhb3	A	G	18: 37,301,317	D112G	probably benign	Het
Pdpr	C	A	8: 111,134,734	P787T	probably damaging	Het
Pgm3	C	T	9: 86,569,233	V123I	probably benign	Het
Pms1	A	C	1: 53,192,098		probably null	Het
Prl2b1	A	G	13: 27,388,566	S14P	possibly damaging	Het
Prune2	T	A	19: 17,199,878	W212R	probably damaging	Het
Rabgef1	A	G	5: 130,213,021	E422G	probably benign	Het
Ralyl	A	G	3: 14,143,412	E204G	probably damaging	Het
Rbpms2	ACTGCTGCTGCTGCTGC	ACTGCTGCTGCTGCTGCTGC	9: 65,651,666		probably benign	Het
Rbpms2	TGCCGCCGCC	TGCCGCCGCCGCC	9: 65,651,680		probably benign	Het
Rit1	C	G	3: 88,729,170	T127S	probably damaging	Het
Slc16a7	C	T	10: 125,231,198	V191M	probably damaging	Het
Slc34a2	A	T	5: 53,058,436	H63L	probably benign	Het
Sp3	A	G	2: 72,938,176	S748P	possibly damaging	Het
Spata31d1b	G	A	13: 59,715,857	C273Y	probably benign	Het
Spata31d1b	G	A	13: 59,717,465	R809K	probably benign	Het
Tmco5	A	T	2: 116,880,879	E90V	probably damaging	Het
Tnxb	A	T	17: 34,678,910	D844V	probably damaging	Het
Tpi1	T	C	6: 124,814,152	T41A	probably benign	Het
Ttn	T	C	2: 76,727,192	I29853V	probably damaging	Het
Vmn2r26	C	T	6: 124,024,771	T5I	probably benign	Het
Wdr95	A	G	5: 149,599,366	D663G	probably benign	Het
Zbtb39	T	C	10: 127,742,700	F381S	probably damaging	Het
Zfp523	T	A	17: 28,194,993	I34N	probably damaging	Het
Zfp646	T	A	7: 127,879,739	Y363N	probably damaging	Het
Zfp712	A	C	13: 67,042,047	C139G	probably damaging	Het
Zfp958	A	G	8: 4,628,590	H205R	probably damaging	Het
Zfp974	G	A	7: 27,910,356	P648L	possibly damaging	Het

Other mutations in Smpd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00944:Smpd4	APN	16	17642757	missense	probably benign	0.04
IGL01461:Smpd4	APN	16	17621506	missense	probably damaging	1.00
IGL02051:Smpd4	APN	16	17626518	missense	probably damaging	1.00
IGL02492:Smpd4	APN	16	17639351	missense	probably damaging	1.00
IGL03181:Smpd4	APN	16	17625807	nonsense	probably null
Victim	UTSW	16	17640971	missense	probably damaging	1.00
weakling	UTSW	16	17638486	intron	probably benign
G1citation:Smpd4	UTSW	16	17640233	missense	probably damaging	1.00
R0197:Smpd4	UTSW	16	17641597	critical splice donor site	probably null
R0549:Smpd4	UTSW	16	17639312	missense	probably benign	0.15
R0789:Smpd4	UTSW	16	17625826	missense	probably benign	0.14
R1077:Smpd4	UTSW	16	17623969	missense	probably damaging	1.00
R1120:Smpd4	UTSW	16	17638486	intron	probably benign
R1716:Smpd4	UTSW	16	17642501	missense	probably damaging	1.00
R1758:Smpd4	UTSW	16	17626008	missense	probably damaging	0.99
R1758:Smpd4	UTSW	16	17640880	missense	probably damaging	1.00
R2115:Smpd4	UTSW	16	17626865	missense	probably benign	0.33
R2849:Smpd4	UTSW	16	17642212	missense	probably damaging	1.00
R4654:Smpd4	UTSW	16	17642128	intron	probably benign
R6157:Smpd4	UTSW	16	17641066	splice site	probably null
R6190:Smpd4	UTSW	16	17632013	missense	probably damaging	1.00
R6822:Smpd4	UTSW	16	17640233	missense	probably damaging	1.00
R7062:Smpd4	UTSW	16	17640971	missense	probably damaging	1.00
R7305:Smpd4	UTSW	16	17641783	missense	probably damaging	0.99
R7759:Smpd4	UTSW	16	17638633	missense	probably damaging	1.00
R7853:Smpd4	UTSW	16	17642741	missense	probably damaging	1.00
R8187:Smpd4	UTSW	16	17629135	missense	probably damaging	1.00
R8303:Smpd4	UTSW	16	17639331	missense	probably damaging	1.00
R8518:Smpd4	UTSW	16	17641020	missense	possibly damaging	0.89
R8735:Smpd4	UTSW	16	17635546	missense	possibly damaging	0.92
R9075:Smpd4	UTSW	16	17639985	missense	unknown
R9439:Smpd4	UTSW	16	17641587	missense	probably benign
Z1176:Smpd4	UTSW	16	17619586	intron	probably benign
Z1177:Smpd4	UTSW	16	17621441	critical splice acceptor site	probably benign

Predicted Primers

PCR Primer
(F):5'- GTTCACGGAAACATTTTGCTTG -3'
(R):5'- ATCTGGCCTGCAAACTAGAG -3'

Sequencing Primer
(F):5'- CGGAAACATTTTGCTTGCATTAATG -3'
(R):5'- GAACAAACAAGGACTCAGCAGTTG -3'

Posted On

2014-06-23