Mutagenetix > Incidental Mutation

Incidental Mutation 'R0266:Sptlc3'

34904

Institutional Source

Beutler Lab

Gene Symbol

Sptlc3

Ensembl Gene

ENSMUSG00000039092

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Synonyms

C130053K05Rik

MMRRC Submission

038492-MU

Accession Numbers

Essential gene?

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

Stock #

R0266 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

139335833-139478981 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 139437957 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Lysine at position 417 (I417K)

Ref Sequence

ENSEMBL: ENSMUSP00000105710 (fasta)

Gene Model

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

AlphaFold

Q8BG54

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047370
AA Change: I417K

PolyPhen 2 Score 0.929 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: I417K

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

possibly damaging
Transcript: ENSMUST00000110083
AA Change: I417K

PolyPhen 2 Score 0.929 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: I417K

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

0.1795

Coding Region Coverage

1x: 98.3%
3x: 97.2%
10x: 94.9%
20x: 89.8%

Validation Efficiency

100% (79/79)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001K19Rik	A	G	12: 110,635,188 (GRCm39)	S117P	possibly damaging	Het
Aars2	T	C	17: 45,818,436 (GRCm39)		probably benign	Het
Acot11	T	C	4: 106,607,185 (GRCm39)	D466G	probably damaging	Het
Adgrd1	G	A	5: 129,216,658 (GRCm39)	A342T	probably benign	Het
Apbb2	A	T	5: 66,459,954 (GRCm39)	N714K	probably benign	Het
Aqp12	C	A	1: 92,934,572 (GRCm39)	H150N	possibly damaging	Het
Brinp3	T	A	1: 146,558,418 (GRCm39)	L114*	probably null	Het
Ccng2	T	C	5: 93,419,148 (GRCm39)		probably benign	Het
Cd36	T	A	5: 18,003,250 (GRCm39)	R265S	probably benign	Het
Ces4a	T	C	8: 105,868,598 (GRCm39)	L104S	probably benign	Het
Clca4b	T	C	3: 144,628,547 (GRCm39)	I387V	probably damaging	Het
Cul7	T	A	17: 46,965,521 (GRCm39)	H566Q	probably benign	Het
Ddx60	A	T	8: 62,486,527 (GRCm39)	H1646L	possibly damaging	Het
Dntt	T	C	19: 41,047,566 (GRCm39)	I503T	probably damaging	Het
Dynlt1a	T	G	17: 6,367,670 (GRCm39)	E2D	probably benign	Het
Efemp2	G	T	19: 5,528,027 (GRCm39)	C78F	probably damaging	Het
Esco1	T	C	18: 10,594,605 (GRCm39)	E227G	probably benign	Het
Fezf2	T	A	14: 12,342,607 (GRCm38)	K419N	probably damaging	Het
Gm17541	A	T	12: 4,739,487 (GRCm39)		probably benign	Het
Gm2381	G	A	7: 42,469,372 (GRCm39)	Q251*	probably null	Het
Gm4782	T	G	6: 50,587,674 (GRCm39)	S686R	probably damaging	Het
Grin3a	G	A	4: 49,665,501 (GRCm39)	R1045*	probably null	Het
Grm8	T	C	6: 27,285,895 (GRCm39)	Y839C	probably damaging	Het
Gtf3c1	G	A	7: 125,243,306 (GRCm39)	P1766L	possibly damaging	Het
Herc2	T	A	7: 55,856,326 (GRCm39)	H3921Q	probably damaging	Het
Hes6	A	T	1: 91,340,026 (GRCm39)	D143E	possibly damaging	Het
Hmcn2	A	G	2: 31,284,839 (GRCm39)	E2055G	probably benign	Het
Hmcn2	G	A	2: 31,335,365 (GRCm39)		probably benign	Het
Ikzf3	A	G	11: 98,358,143 (GRCm39)	L398P	probably benign	Het
Il10ra	A	T	9: 45,176,950 (GRCm39)	I125N	probably benign	Het
Kcnb2	G	A	1: 15,783,137 (GRCm39)		probably benign	Het
Krt77	T	C	15: 101,777,813 (GRCm39)	R81G	possibly damaging	Het
Lrrc40	T	A	3: 157,747,298 (GRCm39)		probably null	Het
Man1a2	C	T	3: 100,489,350 (GRCm39)	R543Q	probably damaging	Het
Mansc1	T	C	6: 134,587,670 (GRCm39)	D169G	probably benign	Het
Mdn1	T	A	4: 32,741,835 (GRCm39)	S3869T	probably damaging	Het
Mettl14	A	T	3: 123,176,475 (GRCm39)	S58T	probably benign	Het
Mrpl4	T	C	9: 20,914,610 (GRCm39)	V62A	probably benign	Het
Myh3	A	G	11: 66,984,498 (GRCm39)	D1085G	possibly damaging	Het
Myo5c	C	A	9: 75,191,498 (GRCm39)		probably benign	Het
Naalad2	G	T	9: 18,262,239 (GRCm39)		probably benign	Het
Nat3	A	G	8: 68,000,432 (GRCm39)	T104A	probably benign	Het
Nek4	A	G	14: 30,679,253 (GRCm39)	E198G	probably damaging	Het
Olfm1	A	G	2: 28,119,619 (GRCm39)	Y403C	probably damaging	Het
Or5w11	C	A	2: 87,459,626 (GRCm39)	T273K	possibly damaging	Het
Or7e177	A	T	9: 20,212,454 (GRCm39)	R320S	probably benign	Het
Osbpl1a	T	A	18: 13,004,220 (GRCm39)		probably null	Het
Pax7	G	A	4: 139,507,047 (GRCm39)	S330L	possibly damaging	Het
Pcdhb15	C	A	18: 37,608,329 (GRCm39)	D520E	probably damaging	Het
Pgm3	T	C	9: 86,449,586 (GRCm39)	T145A	probably benign	Het
Phox2b	G	A	5: 67,253,968 (GRCm39)		probably null	Het
Pik3r6	A	T	11: 68,417,234 (GRCm39)	R59*	probably null	Het
Pold1	A	G	7: 44,190,449 (GRCm39)		probably benign	Het
Ppp1r21	T	C	17: 88,876,500 (GRCm39)		probably benign	Het
Prl5a1	A	G	13: 28,333,970 (GRCm39)	K158E	possibly damaging	Het
Rag2	T	G	2: 101,460,948 (GRCm39)	C419W	probably damaging	Het
Reln	A	G	5: 22,193,774 (GRCm39)	S1395P	probably damaging	Het
Retnlb	T	G	16: 48,639,022 (GRCm39)	Y74*	probably null	Het
Robo3	A	G	9: 37,333,936 (GRCm39)	S633P	probably damaging	Het
Ryr1	A	G	7: 28,740,104 (GRCm39)	S3941P	probably damaging	Het
Scnn1b	A	G	7: 121,511,698 (GRCm39)	N370S	probably damaging	Het
Slc6a5	C	A	7: 49,588,156 (GRCm39)		probably benign	Het
Sort1	T	A	3: 108,252,247 (GRCm39)	N481K	probably benign	Het
Svil	T	A	18: 5,099,063 (GRCm39)		probably benign	Het
Taf4b	T	C	18: 14,946,134 (GRCm39)		probably benign	Het
Tchp	T	C	5: 114,847,394 (GRCm39)	M71T	possibly damaging	Het
Thsd4	T	A	9: 59,904,417 (GRCm39)	H233L	probably benign	Het
Tmem217	G	T	17: 29,745,573 (GRCm39)	N52K	possibly damaging	Het
Tmem38b	T	C	4: 53,840,765 (GRCm39)	L60S	probably damaging	Het
Uqcrfs1	A	C	13: 30,725,146 (GRCm39)	N131K	probably benign	Het
Vars1	T	A	17: 35,232,845 (GRCm39)	S896R	probably benign	Het
Vmn1r170	A	T	7: 23,305,906 (GRCm39)	M103L	probably benign	Het
Vmn2r22	T	C	6: 123,614,363 (GRCm39)	Y409C	probably damaging	Het
Vmn2r92	C	T	17: 18,388,219 (GRCm39)	A408V	probably damaging	Het
Wdr49	A	T	3: 75,359,103 (GRCm39)	I8N	possibly damaging	Het
Zfp648	T	A	1: 154,080,632 (GRCm39)	Y264N	probably damaging	Het
Zmym1	A	C	4: 126,941,818 (GRCm39)	F857V	possibly damaging	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
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
R4610: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'- TGTCATGTACAAAGGACAAGCTCTGAAA -3'
(R):5'- ACGGACAGCAAGCAAGCATATACATAT -3'

Sequencing Primer
(F):5'- GGACAAGCTCTGAAAATTGTTTGC -3'
(R):5'- agtggtggtggtggtgg -3'

Posted On

2013-05-09