Mutagenetix > Incidental Mutation

Incidental Mutation 'R1077:Smpd4'

85703

Institutional Source

Beutler Lab

Gene Symbol

Smpd4

Ensembl Gene

ENSMUSG00000005899

Gene Name

sphingomyelin phosphodiesterase 4

Synonyms

4122402O22Rik, neutral membrane (neutral sphingomyelinase-3)

MMRRC Submission

039163-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.124) question?

Stock #

R1077 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

17619354-17644828 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 17623969 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 35 (V35A)

Ref Sequence

ENSEMBL: ENSMUSP00000155910 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000163592] [ENSMUST00000163997] [ENSMUST00000165363] [ENSMUST00000167217] [ENSMUST00000169662] [ENSMUST00000170117] [ENSMUST00000171435] [ENSMUST00000170273] [ENSMUST00000170366] [ENSMUST00000172182] [ENSMUST00000232116] [ENSMUST00000231311] [ENSMUST00000231627] [ENSMUST00000231792] [ENSMUST00000232043] [ENSMUST00000231436] [ENSMUST00000231722] [ENSMUST00000232442] [ENSMUST00000232021] [ENSMUST00000231257] [ENSMUST00000231887] [ENSMUST00000232271]

AlphaFold

Q6ZPR5

Predicted Effect

probably damaging
Transcript: ENSMUST00000006053
AA Change: V35A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: V35A

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

probably damaging
Transcript: ENSMUST00000090159
AA Change: V35A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: V35A

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 damaging
Transcript: ENSMUST00000163476
AA Change: V35A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: V35A

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: ENSMUST00000163592
AA Change: V35A

PolyPhen 2 Score 0.653 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000126998
Gene: ENSMUSG00000005899
AA Change: V35A

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	110	2.6e-66	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000163997
AA Change: V35A

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000128595
Gene: ENSMUSG00000005899
AA Change: V35A

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 damaging
Transcript: ENSMUST00000165363
AA Change: V35A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: V35A

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

probably damaging
Transcript: ENSMUST00000167217
AA Change: V35A

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000130570
Gene: ENSMUSG00000005899
AA Change: V35A

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	92	3.4e-51	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167362

Predicted Effect

probably damaging
Transcript: ENSMUST00000169662
AA Change: V35A

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000125819
Gene: ENSMUSG00000005899
AA Change: V35A

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	82	1.8e-46	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000170117
AA Change: V35A

SMART Domains

Protein: ENSMUSP00000132279
Gene: ENSMUSG00000005899
AA Change: V35A

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000171435
AA Change: V35A

PolyPhen 2 Score 0.779 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000131560
Gene: ENSMUSG00000005899
AA Change: V35A

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000170273
AA Change: V35A

PolyPhen 2 Score 0.669 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899
AA Change: V35A

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 damaging
Transcript: ENSMUST00000170366
AA Change: V35A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000130990
Gene: ENSMUSG00000005899
AA Change: V35A

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 damaging
Transcript: ENSMUST00000172182
AA Change: V35A

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000126093
Gene: ENSMUSG00000005899
AA Change: V35A

Domain	Start	End	E-Value	Type
Pfam:mit_SMPDase	8	106	1.4e-51	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170401

Predicted Effect

probably damaging
Transcript: ENSMUST00000232116
AA Change: V35A

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000231311
AA Change: V35A

PolyPhen 2 Score 0.738 (Sensitivity: 0.85; Specificity: 0.92)

Predicted Effect

unknown
Transcript: ENSMUST00000231627
AA Change: V35A

Predicted Effect

probably benign
Transcript: ENSMUST00000231792
AA Change: V35A

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)

Predicted Effect

probably damaging
Transcript: ENSMUST00000232043
AA Change: V35A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

Predicted Effect

probably damaging
Transcript: ENSMUST00000231436
AA Change: V35A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000231722
AA Change: V35A

PolyPhen 2 Score 0.455 (Sensitivity: 0.89; Specificity: 0.90)

Predicted Effect

probably damaging
Transcript: ENSMUST00000232442
AA Change: V35A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000232021
AA Change: V35A

PolyPhen 2 Score 0.617 (Sensitivity: 0.87; Specificity: 0.91)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232468

Predicted Effect

probably benign
Transcript: ENSMUST00000231257

Predicted Effect

probably benign
Transcript: ENSMUST00000231887

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232487

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232417

Predicted Effect

probably benign
Transcript: ENSMUST00000232271

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231949

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231736

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232185

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232578

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.3%
3x: 98.8%
10x: 97.3%
20x: 94.6%

Validation Efficiency

100% (40/40)

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: 40 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921528I07Rik	T	C	9: 114,301,702		noncoding transcript	Het
Apob	A	G	12: 8,006,017	K1500E	probably benign	Het
Atp8b1	A	T	18: 64,573,262	Y225*	probably null	Het
Cdc25c	A	T	18: 34,748,973		probably benign	Het
Ceacam15	T	C	7: 16,672,075	N184D	probably benign	Het
Cntln	T	C	4: 84,996,479	S508P	probably damaging	Het
Dhx34	A	G	7: 16,218,368	S111P	probably damaging	Het
Dst	A	G	1: 34,164,167	E759G	probably damaging	Het
Fis1	G	A	5: 136,965,146	A28T	probably damaging	Het
Fsd1	T	C	17: 55,990,542		probably null	Het
Gm15293	T	A	8: 21,202,433	F90Y	probably benign	Het
Grk6	T	C	13: 55,454,527		probably null	Het
Il23r	A	T	6: 67,473,810	H228Q	probably benign	Het
Kcnh4	C	T	11: 100,752,338	V368I	possibly damaging	Het
Kdr	T	C	5: 75,956,231	E728G	probably damaging	Het
Krt33a	T	A	11: 100,015,937	M71L	probably benign	Het
Lrrc7	T	G	3: 158,161,143	D987A	probably damaging	Het
Naalad2	C	T	9: 18,347,506	R491Q	probably damaging	Het
Nedd4l	A	T	18: 65,167,499		probably benign	Het
Pramel7	A	G	2: 87,491,190	L167S	probably damaging	Het
Prkci	A	G	3: 31,050,192	D568G	probably damaging	Het
Psg18	G	A	7: 18,351,075	T32I	possibly damaging	Het
Ric8b	T	A	10: 84,970,717		probably benign	Het
Rnf213	T	C	11: 119,485,998		probably benign	Het
Rttn	T	C	18: 89,064,249	V1433A	probably damaging	Het
Sbf2	A	T	7: 110,367,172		probably benign	Het
Sdk2	C	T	11: 113,838,646		silent	Het
Sfta2	T	C	17: 35,650,127		probably benign	Het
Slc17a1	T	A	13: 23,878,450		probably benign	Het
Slc6a21	G	A	7: 45,288,202	C314Y	probably benign	Het
Sorl1	T	C	9: 42,014,490	D1182G	probably damaging	Het
Syne2	A	G	12: 76,042,035	I5056V	possibly damaging	Het
Tex14	T	C	11: 87,519,745		probably benign	Het
Tex44	A	G	1: 86,427,055	T229A	probably benign	Het
Tfap2b	T	A	1: 19,234,149	C394*	probably null	Het
Ttk	T	A	9: 83,844,149		probably benign	Het
Vmn2r26	G	A	6: 124,053,913	V536I	probably benign	Het
Wac	A	G	18: 7,921,916	T553A	probably damaging	Het
Wdcp	T	A	12: 4,850,685	H180Q	probably damaging	Het
Wdr33	A	G	18: 31,835,461	H235R	probably benign	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
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
R1838:Smpd4	UTSW	16	17642302	splice site	probably null
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'- GCTGGGACCATGCACCACAC -3'
(R):5'- GTCAGAGGCTCTCAATCTTATTAGCACC -3'

Sequencing Primer
(F):5'- ATGCACCACACTGTGTATTTCTG -3'
(R):5'- gcctcttcctgccttcc -3'

Posted On

2013-11-18