Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00944:Smpd4'

29163

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Smpd4

Ensembl Gene

ENSMUSG00000005899

Gene Name

sphingomyelin phosphodiesterase 4

Synonyms

4122402O22Rik, neutral membrane (neutral sphingomyelinase-3)

Accession Numbers

Essential gene?

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

Stock #

IGL00944

Quality Score

Status

Chromosome

Chromosomal Location

17437218-17462692 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 17460621 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 809 (I809T)

Ref Sequence

ENSEMBL: ENSMUSP00000006053 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000056962] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000163997] [ENSMUST00000165363] [ENSMUST00000170366] [ENSMUST00000170273] [ENSMUST00000170996] [ENSMUST00000170117] [ENSMUST00000182344] [ENSMUST00000182368] [ENSMUST00000182117] [ENSMUST00000232271] [ENSMUST00000232021] [ENSMUST00000231792] [ENSMUST00000231436] [ENSMUST00000231722] [ENSMUST00000231627] [ENSMUST00000232116]

AlphaFold

Q6ZPR5

Predicted Effect

probably benign
Transcript: ENSMUST00000006053
AA Change: I809T

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: I809T

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 benign
Transcript: ENSMUST00000090159
AA Change: I793T

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

SMART Domains

Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: I793T

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 benign
Transcript: ENSMUST00000163476
AA Change: I780T

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

SMART Domains

Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: I780T

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 benign
Transcript: ENSMUST00000163997
AA Change: I559T

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000128595
Gene: ENSMUSG00000005899
AA Change: I559T

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 benign
Transcript: ENSMUST00000165363
AA Change: I779T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: I779T

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

probably benign
Transcript: ENSMUST00000170366
AA Change: I737T

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

SMART Domains

Protein: ENSMUSP00000130990
Gene: ENSMUSG00000005899
AA Change: I737T

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

probably benign
Transcript: ENSMUST00000170273
AA Change: I707T

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899
AA Change: I707T

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 benign
Transcript: ENSMUST00000170996
AA Change: I485T

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000129074
Gene: ENSMUSG00000005899
AA Change: I485T

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: ENSMUST00000182526

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166091

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167592

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167362

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170401

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000182822

Predicted Effect

probably benign
Transcript: ENSMUST00000170117

SMART Domains

Protein: ENSMUSP00000132279
Gene: ENSMUSG00000005899

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

Predicted Effect

probably benign
Transcript: ENSMUST00000182671

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: 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: ENSMUST00000183101

Predicted Effect

probably benign
Transcript: ENSMUST00000232271
AA Change: I485T

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

Predicted Effect

probably benign
Transcript: ENSMUST00000232021
AA Change: I707T

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

Predicted Effect

probably benign
Transcript: ENSMUST00000231792
AA Change: I559T

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

Predicted Effect

probably benign
Transcript: ENSMUST00000231436
AA Change: I737T

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

Predicted Effect

probably benign
Transcript: ENSMUST00000231722

Predicted Effect

probably benign
Transcript: ENSMUST00000183279

Predicted Effect

probably benign
Transcript: ENSMUST00000231627

Predicted Effect

probably benign
Transcript: ENSMUST00000182976

Predicted Effect

probably benign
Transcript: ENSMUST00000232116

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232185

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232270

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232468

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231378

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232417

Coding Region Coverage

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: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Atp10b	A	G	11: 43,092,988 (GRCm39)	N441S	probably damaging	Het
Bod1l	A	G	5: 41,974,166 (GRCm39)	C2383R	probably benign	Het
Dapk3	G	T	10: 81,019,910 (GRCm39)		probably null	Het
Dock6	T	C	9: 21,757,930 (GRCm39)	D58G	possibly damaging	Het
Etl4	G	A	2: 20,534,865 (GRCm39)	V107I	possibly damaging	Het
Fam163b	A	G	2: 27,003,597 (GRCm39)	L19P	probably damaging	Het
Fbxl20	A	C	11: 98,004,068 (GRCm39)	F73L	probably damaging	Het
Foxj2	T	C	6: 122,816,594 (GRCm39)	L492P	probably damaging	Het
Hfm1	A	T	5: 107,049,996 (GRCm39)	V391E	possibly damaging	Het
Ift74	T	C	4: 94,581,259 (GRCm39)	Y586H	probably damaging	Het
Klhl12	A	G	1: 134,411,491 (GRCm39)	N280S	probably benign	Het
Lctl	T	A	9: 64,040,411 (GRCm39)	Y292*	probably null	Het
Ltb	C	A	17: 35,413,642 (GRCm39)	Q49K	possibly damaging	Het
Mapk1	T	A	16: 16,853,322 (GRCm39)	D289E	probably benign	Het
Mideas	A	G	12: 84,207,322 (GRCm39)		probably benign	Het
Mroh2b	C	T	15: 4,980,609 (GRCm39)		probably benign	Het
Myot	T	C	18: 44,470,181 (GRCm39)	S53P	possibly damaging	Het
Opn5	G	A	17: 42,922,119 (GRCm39)	L28F	probably damaging	Het
Or5b97	A	T	19: 12,878,719 (GRCm39)	Y142N	probably benign	Het
Or8k39	A	G	2: 86,563,905 (GRCm39)	I17T	possibly damaging	Het
Pals2	T	C	6: 50,140,436 (GRCm39)	V152A	possibly damaging	Het
Pld1	T	A	3: 28,099,247 (GRCm39)		probably null	Het
Rc3h2	A	G	2: 37,288,250 (GRCm39)		probably benign	Het
Robo2	T	A	16: 73,730,585 (GRCm39)	H1009L	possibly damaging	Het
Setd7	T	A	3: 51,440,459 (GRCm39)	D194V	probably damaging	Het
Sh3bp1	A	T	15: 78,789,314 (GRCm39)	D288V	possibly damaging	Het
Spata6	C	T	4: 111,663,125 (GRCm39)		probably benign	Het
Trnau1ap	C	A	4: 132,055,817 (GRCm39)	V30L	possibly damaging	Het
Trpm4	T	C	7: 44,967,773 (GRCm39)	H386R	probably benign	Het
Ttc3	T	G	16: 94,227,620 (GRCm39)		probably null	Het
Ufd1	T	C	16: 18,643,781 (GRCm39)	V180A	possibly damaging	Het
Vmn2r102	A	G	17: 19,899,154 (GRCm39)	I499V	probably damaging	Het
Zfp112	C	A	7: 23,825,021 (GRCm39)	Q330K	probably benign	Het
Zfp668	G	A	7: 127,467,079 (GRCm39)	R166W	probably damaging	Het

Other mutations in Smpd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
R1758:Smpd4	UTSW	16	17,443,872 (GRCm39)	missense	probably damaging	0.99
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

Posted On

2013-04-17