Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02051:Smpd4'

186107

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: 0.081) question?

Stock #

IGL02051

Quality Score

Status

Chromosome

Chromosomal Location

17437218-17462692 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 17444382 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 145 (L145P)

Ref Sequence

ENSEMBL: ENSMUSP00000130720 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000163997] [ENSMUST00000165363] [ENSMUST00000168101] [ENSMUST00000170273] [ENSMUST00000170366] [ENSMUST00000172182] [ENSMUST00000170117] [ENSMUST00000167217] [ENSMUST00000170996] [ENSMUST00000231257] [ENSMUST00000231436] [ENSMUST00000231627] [ENSMUST00000231311] [ENSMUST00000232021] [ENSMUST00000231792] [ENSMUST00000232043] [ENSMUST00000231887] [ENSMUST00000231722] [ENSMUST00000232116] [ENSMUST00000232442] [ENSMUST00000232271]

AlphaFold

Q6ZPR5

Predicted Effect

probably damaging
Transcript: ENSMUST00000006053
AA Change: L145P

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: L145P

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: L145P

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: L145P

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: L145P

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: L145P

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

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 damaging
Transcript: ENSMUST00000165363
AA Change: L145P

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: L145P

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

probably benign
Transcript: ENSMUST00000168101
AA Change: L116P

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000129995
Gene: ENSMUSG00000005899
AA Change: L116P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000170273
AA Change: L72P

PolyPhen 2 Score 0.304 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899
AA Change: L72P

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: ENSMUST00000170366
AA Change: L145P

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000130990
Gene: ENSMUSG00000005899
AA Change: L145P

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

silent
Transcript: ENSMUST00000172182

SMART Domains

Protein: ENSMUSP00000126093
Gene: ENSMUSG00000005899

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167362

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166322

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170401

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: ENSMUST00000167217

SMART Domains

Protein: ENSMUSP00000130570
Gene: ENSMUSG00000005899

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

Predicted Effect

probably benign
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 benign
Transcript: ENSMUST00000231257
AA Change: L116P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000231436
AA Change: L145P

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)

Predicted Effect

probably benign
Transcript: ENSMUST00000231627

Predicted Effect

probably benign
Transcript: ENSMUST00000231311

Predicted Effect

probably benign
Transcript: ENSMUST00000232021
AA Change: L72P

PolyPhen 2 Score 0.259 (Sensitivity: 0.91; Specificity: 0.88)

Predicted Effect

probably benign
Transcript: ENSMUST00000231792

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231736

Predicted Effect

probably benign
Transcript: ENSMUST00000232043

Predicted Effect

probably benign
Transcript: ENSMUST00000231887

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231949

Predicted Effect

probably benign
Transcript: ENSMUST00000231722

Predicted Effect

probably benign
Transcript: ENSMUST00000232116

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232578

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232468

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232417

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232487

Predicted Effect

probably benign
Transcript: ENSMUST00000232442

Predicted Effect

probably benign
Transcript: ENSMUST00000232271

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232185

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: 21 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Cacul1	T	C	19: 60,531,504 (GRCm39)	D255G	probably damaging	Het
Chi3l1	T	C	1: 134,111,887 (GRCm39)	S94P	probably damaging	Het
Defa38	A	G	8: 21,585,275 (GRCm39)		probably benign	Het
Dzip3	T	C	16: 48,792,617 (GRCm39)	T223A	probably benign	Het
Firrm	T	C	1: 163,785,091 (GRCm39)	T763A	probably benign	Het
Gfra3	T	C	18: 34,828,894 (GRCm39)	T167A	possibly damaging	Het
Glb1l3	T	C	9: 26,736,464 (GRCm39)	I533V	probably benign	Het
Gm11437	T	A	11: 84,043,592 (GRCm39)	Q233L	probably benign	Het
Hif1an	A	G	19: 44,551,829 (GRCm39)	Y93C	probably damaging	Het
Hspg2	A	G	4: 137,295,700 (GRCm39)		probably benign	Het
Ints15	A	G	5: 143,293,737 (GRCm39)	C247R	probably damaging	Het
Mak	G	A	13: 41,195,558 (GRCm39)	A385V	probably benign	Het
Mical2	G	T	7: 111,980,597 (GRCm39)	K190N	probably benign	Het
Moxd1	A	G	10: 24,128,916 (GRCm39)		probably null	Het
Ptpn5	A	G	7: 46,732,507 (GRCm39)		probably null	Het
Ryr1	A	G	7: 28,771,083 (GRCm39)	Y2614H	probably benign	Het
Sema3e	T	A	5: 14,274,324 (GRCm39)	Y192N	possibly damaging	Het
Tesk2	A	G	4: 116,608,381 (GRCm39)	E101G	probably damaging	Het
Vmn1r68	A	T	7: 10,261,948 (GRCm39)	V50E	probably benign	Het
Vpreb3	G	A	10: 75,784,244 (GRCm39)		probably null	Het
Vps72	T	C	3: 95,030,040 (GRCm39)	L353P	possibly 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
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

2014-05-07