Mutagenetix > Incidental Mutation

Incidental Mutation 'R4610:Sptlc3'

344578

Institutional Source

Beutler Lab

Gene Symbol

Sptlc3

Ensembl Gene

ENSMUSG00000039092

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Synonyms

C130053K05Rik

MMRRC Submission

041821-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.122) question?

Stock #

R4610 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

139335833-139478981 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 139478600 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 520 (V520I)

Ref Sequence

ENSEMBL: ENSMUSP00000105710 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047370] [ENSMUST00000110083]

AlphaFold

Q8BG54

Predicted Effect

probably benign
Transcript: ENSMUST00000047370
AA Change: V520I

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: V520I

Domain	Start	End	E-Value	Type
transmembrane domain	60	79	N/A	INTRINSIC
Pfam:Aminotran_1_2	160	520	4.8e-59	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000110083
AA Change: V520I

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: V520I

Domain	Start	End	E-Value	Type
transmembrane domain	60	79	N/A	INTRINSIC
Pfam:Aminotran_1_2	160	520	4.8e-59	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134801

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.5%

Validation Efficiency

98% (121/124)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The SPTLC3 gene encodes an isoform of the third subunit of serine palmitoyltransferase (SPT; EC 2.3.1.50), which catalyzes the rate-limiting step of the de novo synthesis of sphingolipids (Hornemann et al., 2006 [PubMed 17023427]). SPT contains 2 main subunits: the common SPTLC1 subunit (MIM 605712) and either SPTLC2 (MIM 605713) or its isoform SPTLC2L (SPTLC3), depending on the tissue in which biosynthesis occurs (Hornemann et al., 2006 [PubMed 17023427]). There are also 2 highly related isoforms of a third subunit, SSSPTA (MIM 613540) and SSSPTB (MIM 610412), that confer acyl-CoA preference of the SPT enzyme and are essential for maximal enzyme activity (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]

Allele List at MGI

Other mutations in this stock

Total: 117 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aars2	T	A	17: 45,827,847 (GRCm39)	D555E	probably damaging	Het
Adgre1	C	A	17: 57,757,073 (GRCm39)	Q777K	possibly damaging	Het
Agpat4	G	A	17: 12,429,264 (GRCm39)		probably null	Het
Ak7	G	A	12: 105,679,834 (GRCm39)	V123M	probably benign	Het
Ankle1	AT	A	8: 71,859,851 (GRCm39)		probably benign	Het
Ankrd44	T	G	1: 54,805,907 (GRCm39)		probably benign	Het
Aprt	A	T	8: 123,302,154 (GRCm39)		probably null	Het
Aptx	T	C	4: 40,702,766 (GRCm39)		probably null	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
AY358078	T	A	14: 52,063,532 (GRCm39)	C393S	possibly damaging	Het
Bbip1	T	C	19: 53,920,606 (GRCm39)	M1V	probably null	Het
Cacng7	T	A	7: 3,385,207 (GRCm39)	M36K	probably benign	Het
Camta1	A	G	4: 151,169,284 (GRCm39)	W156R	probably damaging	Het
Casd1	G	A	6: 4,631,165 (GRCm39)		probably null	Het
Casz1	T	A	4: 149,017,724 (GRCm39)	Y338N	probably damaging	Het
Ccdc66	T	C	14: 27,222,377 (GRCm39)	N122S	probably damaging	Het
Celf2	G	T	2: 6,590,831 (GRCm39)	N279K	possibly damaging	Het
Cfap96	A	T	8: 46,423,505 (GRCm39)	I69N	probably damaging	Het
Cit	A	G	5: 116,132,146 (GRCm39)	T1801A	probably benign	Het
Cnot2	A	G	10: 116,335,323 (GRCm39)	I275T	probably damaging	Het
Ddx4	T	C	13: 112,748,594 (GRCm39)	K435E	probably damaging	Het
Dnajc6	T	C	4: 101,468,461 (GRCm39)	F166L	probably damaging	Het
Dst	T	C	1: 34,208,937 (GRCm39)	L820P	probably damaging	Het
Dusp11	T	A	6: 85,927,037 (GRCm39)	N193Y	probably damaging	Het
Eif1ad7	T	C	12: 88,238,544 (GRCm39)	N72S	probably benign	Het
Eif3m	A	T	2: 104,843,633 (GRCm39)	N116K	probably benign	Het
Epb41l1	A	T	2: 156,351,181 (GRCm39)	E418D	possibly damaging	Het
Esyt2	T	G	12: 116,282,510 (GRCm39)	N153K	probably damaging	Het
Exoc6b	T	G	6: 84,980,141 (GRCm39)		probably benign	Het
Ezr	C	T	17: 7,007,121 (GRCm39)	E502K	possibly damaging	Het
Fbxw11	T	A	11: 32,661,859 (GRCm39)	Y66N	possibly damaging	Het
Frem2	A	G	3: 53,455,228 (GRCm39)	L2116S	possibly damaging	Het
Fry	T	C	5: 150,309,569 (GRCm39)	L671P	probably damaging	Het
Galnt7	A	G	8: 57,998,803 (GRCm39)	I262T	probably damaging	Het
Glp1r	T	C	17: 31,150,221 (GRCm39)	F381S	probably benign	Het
Gm3867	T	C	9: 36,168,567 (GRCm39)		noncoding transcript	Het
Gm8741	G	T	17: 35,555,062 (GRCm39)		noncoding transcript	Het
Golgb1	A	G	16: 36,738,987 (GRCm39)	D2442G	probably damaging	Het
Gp1bb	A	T	16: 18,439,893 (GRCm39)	L67Q	probably damaging	Het
Gstm7	G	A	3: 107,834,235 (GRCm39)	T206I	possibly damaging	Het
H2bc7	A	T	13: 23,758,231 (GRCm39)	V45E	possibly damaging	Het
Hs3st5	A	T	10: 36,704,802 (GRCm39)	D35V	probably benign	Het
Hspa13	T	C	16: 75,558,190 (GRCm39)	H125R	probably benign	Het
Hspa1a	T	G	17: 35,190,156 (GRCm39)	H249P	probably damaging	Het
Igkv10-95	A	T	6: 68,657,562 (GRCm39)	Q6L	probably damaging	Het
Il1rap	T	A	16: 26,533,526 (GRCm39)	L474H	probably benign	Het
Ipo11	T	A	13: 107,016,245 (GRCm39)	Y489F	probably benign	Het
Itga5	A	G	15: 103,259,259 (GRCm39)	Y723H	probably damaging	Het
Itih2	T	C	2: 10,109,971 (GRCm39)	N594S	probably damaging	Het
Itk	T	A	11: 46,227,342 (GRCm39)	Q427L	probably benign	Het
Kif26b	A	G	1: 178,506,920 (GRCm39)	Y332C	probably damaging	Het
Kmt2c	G	A	5: 25,559,382 (GRCm39)	R1086W	probably damaging	Het
Ktn1	T	A	14: 47,963,636 (GRCm39)		probably benign	Het
Lars2	T	A	9: 123,247,758 (GRCm39)	I305N	probably damaging	Het
Lgmn	G	T	12: 102,366,383 (GRCm39)		probably benign	Het
Ltbp4	C	T	7: 27,006,125 (GRCm39)	E1453K	probably damaging	Het
Lypd8	G	A	11: 58,277,675 (GRCm39)	M152I	probably benign	Het
Man2a1	T	A	17: 65,019,454 (GRCm39)	S773T	probably benign	Het
Map2k6	T	G	11: 110,390,300 (GRCm39)	L278R	probably damaging	Het
Mbtps1	A	T	8: 120,262,086 (GRCm39)	D354E	probably damaging	Het
Mcpt9	C	T	14: 56,266,049 (GRCm39)	V60M	probably damaging	Het
Mical3	C	A	6: 120,911,799 (GRCm39)	E1083*	probably null	Het
Mms19	A	G	19: 41,933,935 (GRCm39)	V811A	possibly damaging	Het
Mrc2	G	A	11: 105,239,257 (GRCm39)		probably null	Het
Mslnl	G	A	17: 25,961,908 (GRCm39)	V128M	probably damaging	Het
Mtcl1	T	A	17: 66,684,882 (GRCm39)	H520L	probably benign	Het
Mymk	A	T	2: 26,952,719 (GRCm39)	F130I	probably damaging	Het
Myo1f	C	T	17: 33,801,306 (GRCm39)	R333C	probably damaging	Het
Myo9a	T	A	9: 59,779,165 (GRCm39)	H1640Q	probably benign	Het
Nav1	A	G	1: 135,520,186 (GRCm39)		probably benign	Het
Ncbp3	G	T	11: 72,969,844 (GRCm39)	G564C	probably damaging	Het
Ncoa4	A	T	14: 31,898,682 (GRCm39)	I501L	probably benign	Het
Ngp	T	A	9: 110,249,883 (GRCm39)	N60K	possibly damaging	Het
Npc1l1	G	T	11: 6,178,215 (GRCm39)	D398E	probably damaging	Het
Nphs2	T	A	1: 156,153,701 (GRCm39)	M264K	probably damaging	Het
Or4s2b	G	A	2: 88,508,240 (GRCm39)	V14I	probably benign	Het
Or4s2b	T	G	2: 88,508,523 (GRCm39)	V101G	probably benign	Het
Or7e165	T	A	9: 19,694,442 (GRCm39)	Y4*	probably null	Het
Or8b8	T	A	9: 37,809,622 (GRCm39)	S307R	probably benign	Het
Patz1	A	G	11: 3,256,241 (GRCm39)	Y509C	probably damaging	Het
Pax8	G	A	2: 24,311,595 (GRCm39)	P447S	probably damaging	Het
Pde11a	A	G	2: 75,988,677 (GRCm39)	V488A	probably benign	Het
Pex11g	C	T	8: 3,515,899 (GRCm39)	V45M	probably benign	Het
Pik3ip1	T	A	11: 3,283,327 (GRCm39)	S142R	probably damaging	Het
Pitpnm2	C	G	5: 124,263,434 (GRCm39)	A819P	probably damaging	Het
Pla2g4e	T	G	2: 120,016,863 (GRCm39)	H226P	possibly damaging	Het
Plin4	T	A	17: 56,412,418 (GRCm39)	M538L	probably benign	Het
Ppp3cb	T	C	14: 20,570,714 (GRCm39)	N339S	possibly damaging	Het
Rev1	T	C	1: 38,092,730 (GRCm39)	E1202G	probably damaging	Het
Rngtt	T	A	4: 33,339,133 (GRCm39)		probably benign	Het
Serpinb12	T	A	1: 106,876,883 (GRCm39)	D66E	probably benign	Het
Sgsm1	A	T	5: 113,403,173 (GRCm39)	F958Y	probably damaging	Het
Slc35e2	T	C	4: 155,702,106 (GRCm39)	F290S	probably benign	Het
Sorl1	C	T	9: 41,943,210 (GRCm39)	V889M	possibly damaging	Het
Stam	A	T	2: 14,120,669 (GRCm39)	H53L	probably damaging	Het
Stox2	A	G	8: 47,645,970 (GRCm39)	S497P	probably damaging	Het
Tarbp1	A	G	8: 127,201,069 (GRCm39)	Y246H	probably damaging	Het
Tbx15	A	G	3: 99,259,683 (GRCm39)	Y518C	probably damaging	Het
Tdrd5	T	A	1: 156,111,944 (GRCm39)	T479S	probably benign	Het
Tescl	T	C	7: 24,032,683 (GRCm39)	E214G	probably damaging	Het
Tex10	T	C	4: 48,452,946 (GRCm39)	D671G	probably benign	Het
Tmem132d	A	G	5: 128,061,360 (GRCm39)	V414A	probably benign	Het
Tmem41b	T	A	7: 109,573,941 (GRCm39)		probably benign	Het
Tnfrsf18	A	G	4: 156,106,337 (GRCm39)		probably benign	Het
Tulp4	T	A	17: 6,249,108 (GRCm39)	D42E	probably damaging	Het
Ubtd1	A	G	19: 42,022,103 (GRCm39)	N125S	probably damaging	Het
Ubxn4	T	A	1: 128,183,186 (GRCm39)	F68I	probably benign	Het
Urb1	A	G	16: 90,573,159 (GRCm39)	S958P	probably benign	Het
Vash2	T	C	1: 190,692,498 (GRCm39)	S226G	probably benign	Het
Vmn2r120	C	T	17: 57,816,120 (GRCm39)	G745E	probably damaging	Het
Vmn2r58	T	A	7: 41,487,117 (GRCm39)	I593F	probably benign	Het
Zfp398	T	C	6: 47,817,361 (GRCm39)	L67P	probably damaging	Het
Zfp607b	T	A	7: 27,403,120 (GRCm39)	H525Q	probably damaging	Het
Zfp629	T	C	7: 127,211,492 (GRCm39)	T106A	probably benign	Het
Zfp980	G	A	4: 145,428,653 (GRCm39)	G461S	probably benign	Het
Zic5	T	A	14: 122,702,212 (GRCm39)	D173V	probably damaging	Het
Zranb2	G	A	3: 157,247,521 (GRCm39)		probably benign	Het

Other mutations in Sptlc3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01392:Sptlc3	APN	2	139,388,341 (GRCm39)	missense	possibly damaging	0.55
IGL01537:Sptlc3	APN	2	139,431,615 (GRCm39)	missense	possibly damaging	0.95
IGL01996:Sptlc3	APN	2	139,423,424 (GRCm39)	splice site	probably benign
IGL02512:Sptlc3	APN	2	139,389,123 (GRCm39)	missense	probably damaging	1.00
IGL03278:Sptlc3	APN	2	139,431,579 (GRCm39)	missense	probably damaging	1.00
IGL03286:Sptlc3	APN	2	139,431,579 (GRCm39)	missense	probably damaging	1.00
R0266:Sptlc3	UTSW	2	139,437,957 (GRCm39)	missense	possibly damaging	0.93
R0362:Sptlc3	UTSW	2	139,388,475 (GRCm39)	splice site	probably benign
R1464:Sptlc3	UTSW	2	139,389,154 (GRCm39)	missense	probably benign	0.00
R1464:Sptlc3	UTSW	2	139,389,154 (GRCm39)	missense	probably benign	0.00
R1494:Sptlc3	UTSW	2	139,431,480 (GRCm39)	missense	possibly damaging	0.58
R1847:Sptlc3	UTSW	2	139,467,843 (GRCm39)	missense	probably benign	0.08
R1919:Sptlc3	UTSW	2	139,408,595 (GRCm39)	missense	possibly damaging	0.66
R2093:Sptlc3	UTSW	2	139,467,794 (GRCm39)	missense	possibly damaging	0.89
R2396:Sptlc3	UTSW	2	139,408,506 (GRCm39)	missense	probably benign	0.44
R2972:Sptlc3	UTSW	2	139,431,581 (GRCm39)	missense	probably damaging	1.00
R2973:Sptlc3	UTSW	2	139,431,581 (GRCm39)	missense	probably damaging	1.00
R2974:Sptlc3	UTSW	2	139,431,581 (GRCm39)	missense	probably damaging	1.00
R4601:Sptlc3	UTSW	2	139,478,600 (GRCm39)	missense	probably benign	0.01
R4602:Sptlc3	UTSW	2	139,478,600 (GRCm39)	missense	probably benign	0.01
R4745:Sptlc3	UTSW	2	139,389,087 (GRCm39)	missense	probably damaging	1.00
R4779:Sptlc3	UTSW	2	139,431,509 (GRCm39)	missense	probably benign	0.04
R4992:Sptlc3	UTSW	2	139,437,923 (GRCm39)	missense	probably benign	0.04
R5162:Sptlc3	UTSW	2	139,473,263 (GRCm39)	missense	probably benign	0.11
R5401:Sptlc3	UTSW	2	139,478,643 (GRCm39)	missense	possibly damaging	0.75
R5406:Sptlc3	UTSW	2	139,388,398 (GRCm39)	missense	probably benign	0.26
R5642:Sptlc3	UTSW	2	139,388,328 (GRCm39)	missense	probably damaging	0.96
R5840:Sptlc3	UTSW	2	139,389,126 (GRCm39)	missense	probably damaging	1.00
R6057:Sptlc3	UTSW	2	139,423,533 (GRCm39)	missense	probably damaging	0.99
R6376:Sptlc3	UTSW	2	139,478,692 (GRCm39)	missense	probably benign	0.21
R6852:Sptlc3	UTSW	2	139,408,506 (GRCm39)	missense	probably benign	0.44
R7026:Sptlc3	UTSW	2	139,379,608 (GRCm39)	missense	probably benign
R7412:Sptlc3	UTSW	2	139,431,537 (GRCm39)	missense	possibly damaging	0.75
R7516:Sptlc3	UTSW	2	139,431,438 (GRCm39)	missense	probably benign	0.11
R7733:Sptlc3	UTSW	2	139,473,288 (GRCm39)	missense	possibly damaging	0.77
R7826:Sptlc3	UTSW	2	139,389,115 (GRCm39)	missense	probably benign	0.44
R7949:Sptlc3	UTSW	2	139,467,795 (GRCm39)	missense	possibly damaging	0.81
R9224:Sptlc3	UTSW	2	139,336,154 (GRCm39)	missense	probably benign	0.17
R9237:Sptlc3	UTSW	2	139,408,605 (GRCm39)	missense	probably benign	0.40
R9319:Sptlc3	UTSW	2	139,478,730 (GRCm39)	missense	possibly damaging	0.65
R9330:Sptlc3	UTSW	2	139,388,423 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- ACACTCACAATGTTGAGTTAGAGC -3'
(R):5'- TGAAATTGTCCTCAGAAGGGG -3'

Sequencing Primer
(F):5'- ATTACTGGAGCATACTGGCC -3'
(R):5'- TTGTCCTCAGAAGGGGTAAAATAC -3'

Posted On

2015-09-25