Mutagenetix > Incidental Mutation

Incidental Mutation 'R4411:Smpd5'

327938

Institutional Source

Beutler Lab

Gene Symbol

Smpd5

Ensembl Gene

ENSMUSG00000071724

Gene Name

sphingomyelin phosphodiesterase 5

Synonyms

Gm10345

MMRRC Submission

041693-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.159) question?

Stock #

R4411 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

76178548-76181096 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 76179112 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 160 (R160L)

Ref Sequence

ENSEMBL: ENSMUSP00000134687 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023222] [ENSMUST00000074173] [ENSMUST00000163991] [ENSMUST00000230221] [ENSMUST00000171192] [ENSMUST00000171340]

AlphaFold

D6MZJ6

Predicted Effect

probably benign
Transcript: ENSMUST00000023222

SMART Domains

Protein: ENSMUSP00000023222
Gene: ENSMUSG00000022562

Domain	Start	End	E-Value	Type
Pfam:Hydant_A_N	9	212	1.5e-63	PFAM
Pfam:Hydantoinase_A	231	531	6.4e-109	PFAM
low complexity region	629	637	N/A	INTRINSIC
Pfam:Hydantoinase_B	734	1256	5.2e-225	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000074173

SMART Domains

Protein: ENSMUSP00000073805
Gene: ENSMUSG00000049653

Domain	Start	End	E-Value	Type
Pfam:Speriolin_N	1	176	5.1e-67	PFAM
Pfam:Speriolin_N	172	262	1.2e-25	PFAM
Pfam:Speriolin_C	334	480	1.5e-66	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000096370

Predicted Effect

possibly damaging
Transcript: ENSMUST00000163991
AA Change: R160L

PolyPhen 2 Score 0.746 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000134687
Gene: ENSMUSG00000071724
AA Change: R160L

Domain	Start	End	E-Value	Type
transmembrane domain	77	99	N/A	INTRINSIC
Pfam:Exo_endo_phos	176	471	4.1e-11	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167433

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169664

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170261

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175428

Predicted Effect

probably benign
Transcript: ENSMUST00000230221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230735

Predicted Effect

probably benign
Transcript: ENSMUST00000171192

SMART Domains

Protein: ENSMUSP00000133693
Gene: ENSMUSG00000071724

Domain	Start	End	E-Value	Type
low complexity region	35	46	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000171340

SMART Domains

Protein: ENSMUSP00000129100
Gene: ENSMUSG00000022562

Domain	Start	End	E-Value	Type
Pfam:Hydant_A_N	9	212	2.8e-60	PFAM
Pfam:Hydantoinase_A	231	531	6.6e-102	PFAM
low complexity region	629	637	N/A	INTRINSIC
Pfam:Hydantoinase_B	733	1260	8.2e-190	PFAM

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.9%

Validation Efficiency

95% (62/65)

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	T	C	11: 110,042,781 (GRCm39)	I423V	probably benign	Het
Abl2	T	C	1: 156,457,652 (GRCm39)	V306A	possibly damaging	Het
Adcy4	T	C	14: 56,006,900 (GRCm39)	Y1006C	probably damaging	Het
Adprhl1	T	C	8: 13,296,114 (GRCm39)	K144E	probably benign	Het
Arid5b	T	C	10: 67,932,519 (GRCm39)	R885G	probably damaging	Het
Atp9a	A	T	2: 168,503,853 (GRCm39)	V613E	probably damaging	Het
Atxn7l1	G	T	12: 33,244,886 (GRCm39)		probably benign	Het
Brd8	C	A	18: 34,756,497 (GRCm39)		probably benign	Het
Bsnd	C	T	4: 106,343,868 (GRCm39)	R146H	probably benign	Het
C4b	C	T	17: 34,947,838 (GRCm39)	R1659H	probably damaging	Het
Duox1	G	A	2: 122,168,115 (GRCm39)	R1080H	probably benign	Het
Eml2	T	C	7: 18,916,326 (GRCm39)		probably null	Het
Fbxo44	G	A	4: 148,238,065 (GRCm39)	R221C	probably damaging	Het
Frem1	T	C	4: 82,881,481 (GRCm39)	D166G	probably damaging	Het
Galnt5	T	C	2: 57,889,207 (GRCm39)	L269P	probably benign	Het
Gigyf2	A	G	1: 87,364,582 (GRCm39)	E954G	probably damaging	Het
Gpc6	T	C	14: 118,188,590 (GRCm39)	V408A	probably benign	Het
Hspg2	A	G	4: 137,289,535 (GRCm39)	T3832A	probably benign	Het
Ift88	A	G	14: 57,715,436 (GRCm39)	N493S	probably damaging	Het
Ighv1-76	A	T	12: 115,811,731 (GRCm39)	C41S	probably damaging	Het
Igkv12-46	G	A	6: 69,741,930 (GRCm39)	T16I	probably benign	Het
Igkv3-9	G	T	6: 70,565,547 (GRCm39)	V49F	probably damaging	Het
Isoc2b	A	T	7: 4,852,433 (GRCm39)		probably benign	Het
Lcp2	T	A	11: 34,037,173 (GRCm39)		probably benign	Het
Lmntd1	A	G	6: 145,373,003 (GRCm39)		probably null	Het
Mdm2	A	T	10: 117,545,694 (GRCm39)		probably null	Het
Mrgprx3-ps	T	C	7: 46,959,746 (GRCm39)		noncoding transcript	Het
Msh2	T	C	17: 88,025,032 (GRCm39)	S637P	probably damaging	Het
Myo5b	T	C	18: 74,831,345 (GRCm39)	F765S	possibly damaging	Het
Nav2	T	A	7: 49,047,857 (GRCm39)	N91K	probably benign	Het
Ndor1	G	A	2: 25,138,492 (GRCm39)	P363S	probably benign	Het
Npr3	G	C	15: 11,905,235 (GRCm39)	T164R	probably benign	Het
Pcdhb5	T	C	18: 37,455,050 (GRCm39)	S477P	possibly damaging	Het
Pde3b	GTGATGATGATGATGATGATGATGATG	GTGATGATGATGATGATGATGATG	7: 114,133,984 (GRCm39)		probably benign	Het
Pnpla7	G	A	2: 24,941,716 (GRCm39)	W13*	probably null	Het
Pnpla8	T	C	12: 44,330,225 (GRCm39)	V41A	probably benign	Het
Prdm2	A	T	4: 142,860,240 (GRCm39)	S1017T	probably benign	Het
Prdm5	T	A	6: 65,878,771 (GRCm39)	Y108*	probably null	Het
Rab34	T	A	11: 78,079,592 (GRCm39)		probably null	Het
Skic3	A	G	13: 76,275,623 (GRCm39)	E410G	possibly damaging	Het
Spmip10	A	G	18: 56,727,720 (GRCm39)	T65A	probably benign	Het
Srrm2	A	G	17: 24,029,442 (GRCm39)		probably benign	Het
Taf5	T	A	19: 47,059,453 (GRCm39)	V199D	probably damaging	Het
Tas2r114	C	T	6: 131,666,585 (GRCm39)	V148I	probably benign	Het
Tas2r136	C	A	6: 132,754,972 (GRCm39)	V52L	probably damaging	Het
Tnfrsf25	G	A	4: 152,202,843 (GRCm39)		probably benign	Het
Tpd52l1	T	C	10: 31,255,315 (GRCm39)	T11A	possibly damaging	Het
Trmt1l	G	A	1: 151,327,905 (GRCm39)	E472K	probably benign	Het
Ttc17	T	C	2: 94,173,098 (GRCm39)	K766E	probably damaging	Het
Ttn	C	T	2: 76,560,633 (GRCm39)	R29256Q	probably damaging	Het
Ttn	T	C	2: 76,572,414 (GRCm39)	I26160V	probably damaging	Het
Ubxn6	A	T	17: 56,376,303 (GRCm39)	V311E	probably damaging	Het
Usp2	T	C	9: 44,002,360 (GRCm39)	S351P	probably damaging	Het
Usp7	C	A	16: 8,526,778 (GRCm39)	D187Y	probably damaging	Het
Vmn1r115	C	T	7: 20,578,207 (GRCm39)	R235K	probably benign	Het
Vmn2r50	A	C	7: 9,784,235 (GRCm39)	F80V	probably damaging	Het
Vmn2r58	T	A	7: 41,511,360 (GRCm39)	K481M	possibly damaging	Het
Vmn2r86	A	G	10: 130,288,469 (GRCm39)	I344T	possibly damaging	Het
Zfp455	A	T	13: 67,355,389 (GRCm39)	N219I	probably damaging	Het

Other mutations in Smpd5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R4475:Smpd5	UTSW	15	76,178,926 (GRCm39)	missense	probably damaging	1.00
R4715:Smpd5	UTSW	15	76,179,893 (GRCm39)	missense	probably benign	0.04
R4745:Smpd5	UTSW	15	76,179,008 (GRCm39)	missense	probably benign	0.04
R4879:Smpd5	UTSW	15	76,179,070 (GRCm39)	missense	possibly damaging	0.72
R5409:Smpd5	UTSW	15	76,179,914 (GRCm39)	missense	probably damaging	0.99
R5533:Smpd5	UTSW	15	76,178,757 (GRCm39)	missense	possibly damaging	0.47
R5579:Smpd5	UTSW	15	76,179,325 (GRCm39)	missense	possibly damaging	0.90
R6076:Smpd5	UTSW	15	76,179,092 (GRCm39)	missense	probably damaging	1.00
R7531:Smpd5	UTSW	15	76,180,539 (GRCm39)	missense	probably benign	0.00
R7826:Smpd5	UTSW	15	76,180,496 (GRCm39)	missense	probably benign	0.00
R8184:Smpd5	UTSW	15	76,179,926 (GRCm39)	missense	probably benign	0.00
Z1177:Smpd5	UTSW	15	76,180,501 (GRCm39)	missense	possibly damaging	0.66
Z1177:Smpd5	UTSW	15	76,180,451 (GRCm39)	missense	possibly damaging	0.84

Predicted Primers

PCR Primer
(F):5'- AAGTGGGGTGTTGCTACCAC -3'
(R):5'- TTGGTACCAAGACACGCAC -3'

Sequencing Primer
(F):5'- CTACCCTTAGCGTTGGTCGG -3'
(R):5'- CGCACAAGACGACGAGCTG -3'

Posted On

2015-07-07