Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01461:Smpd4'

87977

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 #

IGL01461

Quality Score

Status

Chromosome

Chromosomal Location

17437218-17462692 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 17439370 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Proline at position 7 (Q7P)

Ref Sequence

ENSEMBL: ENSMUSP00000155897 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006053] [ENSMUST00000090159] [ENSMUST00000163476] [ENSMUST00000163592] [ENSMUST00000163997] [ENSMUST00000165092] [ENSMUST00000170117] [ENSMUST00000169662] [ENSMUST00000170273] [ENSMUST00000165363] [ENSMUST00000170366] [ENSMUST00000168101] [ENSMUST00000172182] [ENSMUST00000171435] [ENSMUST00000167217] [ENSMUST00000170996] [ENSMUST00000232442] [ENSMUST00000231257] [ENSMUST00000231436] [ENSMUST00000231792] [ENSMUST00000231887] [ENSMUST00000232043] [ENSMUST00000232116] [ENSMUST00000231627] [ENSMUST00000231722] [ENSMUST00000231311] [ENSMUST00000232021] [ENSMUST00000232271]

AlphaFold

Q6ZPR5

Predicted Effect

probably damaging
Transcript: ENSMUST00000006053
AA Change: Q7P

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

SMART Domains

Protein: ENSMUSP00000006053
Gene: ENSMUSG00000005899
AA Change: Q7P

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: Q7P

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

SMART Domains

Protein: ENSMUSP00000087620
Gene: ENSMUSG00000005899
AA Change: Q7P

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: Q7P

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

SMART Domains

Protein: ENSMUSP00000131867
Gene: ENSMUSG00000005899
AA Change: Q7P

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 damaging
Transcript: ENSMUST00000163592
AA Change: Q7P

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

SMART Domains

Protein: ENSMUSP00000126998
Gene: ENSMUSG00000005899
AA Change: Q7P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000163997
AA Change: Q7P

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000128595
Gene: ENSMUSG00000005899
AA Change: Q7P

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: ENSMUST00000165092
AA Change: Q7P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000170117
AA Change: Q7P

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

SMART Domains

Protein: ENSMUSP00000132279
Gene: ENSMUSG00000005899
AA Change: Q7P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000169662
AA Change: Q7P

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

SMART Domains

Protein: ENSMUSP00000125819
Gene: ENSMUSG00000005899
AA Change: Q7P

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000170273
AA Change: Q7P

PolyPhen 2 Score 0.533 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000129957
Gene: ENSMUSG00000005899
AA Change: Q7P

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: ENSMUST00000165363
AA Change: Q7P

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

SMART Domains

Protein: ENSMUSP00000130720
Gene: ENSMUSG00000005899
AA Change: Q7P

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 damaging
Transcript: ENSMUST00000170366
AA Change: Q7P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000130990
Gene: ENSMUSG00000005899
AA Change: Q7P

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: ENSMUST00000168101
AA Change: Q7P

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

SMART Domains

Protein: ENSMUSP00000129995
Gene: ENSMUSG00000005899
AA Change: Q7P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000172182
AA Change: Q7P

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000126093
Gene: ENSMUSG00000005899
AA Change: Q7P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000171435
AA Change: Q7P

PolyPhen 2 Score 0.053 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000131560
Gene: ENSMUSG00000005899
AA Change: Q7P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000167217
AA Change: Q7P

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

SMART Domains

Protein: ENSMUSP00000130570
Gene: ENSMUSG00000005899
AA Change: Q7P

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167362

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170401

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166322

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166091

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 damaging
Transcript: ENSMUST00000232442
AA Change: Q7P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000231257
AA Change: Q7P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Predicted Effect

probably damaging
Transcript: ENSMUST00000231436
AA Change: Q7P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Predicted Effect

probably benign
Transcript: ENSMUST00000231792
AA Change: Q7P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000231887
AA Change: Q7P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000232043
AA Change: Q7P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000232116
AA Change: Q7P

PolyPhen 2 Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)

Predicted Effect

unknown
Transcript: ENSMUST00000231627
AA Change: Q7P

Predicted Effect

possibly damaging
Transcript: ENSMUST00000231722
AA Change: Q7P

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)

Predicted Effect

probably benign
Transcript: ENSMUST00000231311
AA Change: Q7P

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000232021
AA Change: Q7P

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232417

Predicted Effect

probably benign
Transcript: ENSMUST00000232271

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232578

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231949

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232185

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000231736

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232468

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: 28 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	T	C	13: 77,429,214 (GRCm39)	F767S	probably benign	Het
Abca13	A	G	11: 9,353,834 (GRCm39)	T3719A	probably damaging	Het
Apob	A	T	12: 8,051,884 (GRCm39)	M1137L	probably benign	Het
Brd9	C	T	13: 74,099,717 (GRCm39)	Q445*	probably null	Het
Cdh23	T	C	10: 60,244,926 (GRCm39)	T990A	possibly damaging	Het
Cenpf	A	G	1: 189,389,293 (GRCm39)	L1513S	probably damaging	Het
Col27a1	A	G	4: 63,142,480 (GRCm39)	K56R	probably damaging	Het
Cryaa	A	G	17: 31,900,000 (GRCm39)	Y118C	probably damaging	Het
Dtl	T	C	1: 191,278,729 (GRCm39)	T378A	possibly damaging	Het
E330020D12Rik	A	G	1: 153,284,105 (GRCm39)		noncoding transcript	Het
F7	A	G	8: 13,082,245 (GRCm39)	D145G	possibly damaging	Het
Flvcr2	A	G	12: 85,849,905 (GRCm39)		probably benign	Het
Hltf	A	T	3: 20,154,103 (GRCm39)	K680*	probably null	Het
Ing1	T	G	8: 11,611,453 (GRCm39)	F22V	probably benign	Het
Ipo5	A	G	14: 121,165,945 (GRCm39)	D330G	probably damaging	Het
Itgax	G	T	7: 127,734,190 (GRCm39)	D321Y	probably damaging	Het
Kel	A	C	6: 41,678,845 (GRCm39)		probably null	Het
Marchf10	T	C	11: 105,280,431 (GRCm39)	K618R	probably damaging	Het
Mast4	T	A	13: 102,890,576 (GRCm39)	M925L	probably damaging	Het
Miga1	C	T	3: 152,040,934 (GRCm39)	E78K	probably damaging	Het
Or4c106	G	T	2: 88,682,669 (GRCm39)	C125F	probably damaging	Het
Or7e165	T	A	9: 19,695,245 (GRCm39)		probably null	Het
Pkdrej	T	C	15: 85,704,575 (GRCm39)	I454V	possibly damaging	Het
Poglut2	T	C	1: 44,150,094 (GRCm39)	Q365R	probably damaging	Het
Prpf6	C	A	2: 181,273,304 (GRCm39)	T283N	probably benign	Het
R3hdm1	A	G	1: 128,106,643 (GRCm39)	H197R	probably damaging	Het
Resf1	T	C	6: 149,233,013 (GRCm39)		probably benign	Het
Vmn2r84	A	T	10: 130,227,094 (GRCm39)	I248K	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
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

2013-11-18