Mutagenetix > Incidental Mutation

Incidental Mutation 'R6376:Sptlc3'

514955

Institutional Source

Beutler Lab

Gene Symbol

Sptlc3

Ensembl Gene

ENSMUSG00000039092

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Synonyms

C130053K05Rik

MMRRC Submission

044526-MU

Accession Numbers

Essential gene?

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

Stock #

R6376 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

139335833-139478981 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 139478692 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 550 (N550K)

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: N550K

PolyPhen 2 Score 0.210 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: N550K

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: N550K

PolyPhen 2 Score 0.210 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: N550K

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: 100.0%
3x: 99.9%
10x: 99.4%
20x: 97.8%

Validation Efficiency

100% (81/81)

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930550C14Rik	A	T	9: 53,339,456 (GRCm39)	E106D	probably damaging	Het
A830018L16Rik	A	T	1: 11,868,718 (GRCm39)	N333Y	probably damaging	Het
Abca4	T	A	3: 121,917,309 (GRCm39)	M1007K	possibly damaging	Het
Accsl	T	A	2: 93,687,343 (GRCm39)	I495F	probably damaging	Het
Acsl3	T	C	1: 78,674,182 (GRCm39)	S373P	possibly damaging	Het
Adam7	A	G	14: 68,742,546 (GRCm39)	I689T	possibly damaging	Het
Akap11	G	A	14: 78,752,336 (GRCm39)	T179I	probably damaging	Het
Ankmy1	T	C	1: 92,816,187 (GRCm39)	K309R	possibly damaging	Het
Apaf1	A	T	10: 90,859,673 (GRCm39)	I824N	probably damaging	Het
Apc2	T	A	10: 80,148,488 (GRCm39)	C1152S	probably damaging	Het
Arhgap17	C	A	7: 122,899,727 (GRCm39)	W409L	probably damaging	Het
Arhgef15	T	C	11: 68,845,796 (GRCm39)	I19V	unknown	Het
Arnt	C	A	3: 95,397,936 (GRCm39)	P573H	probably damaging	Het
Arvcf	G	A	16: 18,223,882 (GRCm39)	G932R	probably damaging	Het
Atg4a-ps	C	T	3: 103,553,044 (GRCm39)	W99*	probably null	Het
Atp13a5	T	A	16: 29,056,004 (GRCm39)	D1052V	probably benign	Het
Atp2b4	T	C	1: 133,642,797 (GRCm39)	T1103A	probably damaging	Het
B4galnt4	C	A	7: 140,647,335 (GRCm39)	Q362K	possibly damaging	Het
Cd320	T	A	17: 34,066,491 (GRCm39)	N90K	probably benign	Het
Cep170b	A	T	12: 112,698,502 (GRCm39)	I87F	probably damaging	Het
Coq3	T	G	4: 21,900,486 (GRCm39)	C238G	probably benign	Het
Cpa5	A	T	6: 30,614,044 (GRCm39)	Q62L	probably benign	Het
Ctsg	A	T	14: 56,339,110 (GRCm39)	C49*	probably null	Het
Cul9	T	C	17: 46,819,489 (GRCm39)	T2000A	probably damaging	Het
Dedd	C	T	1: 171,167,790 (GRCm39)	P155S	probably benign	Het
Dnah1	A	G	14: 30,997,565 (GRCm39)	S2598P	probably damaging	Het
Dnah14	C	T	1: 181,433,459 (GRCm39)	P379S	possibly damaging	Het
Dync2h1	A	T	9: 7,165,703 (GRCm39)	S519R	probably benign	Het
Eea1	A	G	10: 95,874,660 (GRCm39)	S1192G	probably benign	Het
Eif5b	T	C	1: 38,084,760 (GRCm39)	I869T	probably damaging	Het
Elavl4	C	A	4: 110,112,651 (GRCm39)		probably benign	Het
Eml2	G	A	7: 18,935,088 (GRCm39)	V432I	probably damaging	Het
Ets2	G	A	16: 95,520,037 (GRCm39)	R421H	probably damaging	Het
Exoc3l2	G	A	7: 19,203,635 (GRCm39)	A76T	possibly damaging	Het
Fam89b	T	C	19: 5,778,757 (GRCm39)	Y144C	probably damaging	Het
Greb1	T	C	12: 16,749,580 (GRCm39)	E1082G	probably damaging	Het
Gtf3a	A	T	5: 146,890,798 (GRCm39)		probably null	Het
Hoxc12	C	A	15: 102,845,524 (GRCm39)	F79L	possibly damaging	Het
Hspb8	G	T	5: 116,547,491 (GRCm39)	L164I	probably damaging	Het
Ina	C	T	19: 47,003,564 (GRCm39)	A124V	probably benign	Het
Inhbb	T	A	1: 119,345,411 (GRCm39)	I293F	probably damaging	Het
Itpr3	A	G	17: 27,314,449 (GRCm39)	Y633C	possibly damaging	Het
Jag2	C	T	12: 112,872,949 (GRCm39)	V1102I	probably benign	Het
Kalrn	A	T	16: 33,796,361 (GRCm39)	F1138Y	probably benign	Het
Large2	T	A	2: 92,200,853 (GRCm39)		probably benign	Het
Lats2	A	G	14: 57,959,966 (GRCm39)	S177P	probably benign	Het
Lims2	G	A	18: 32,087,515 (GRCm39)	R124H	possibly damaging	Het
Lrp2	T	A	2: 69,313,787 (GRCm39)	T2315S	probably benign	Het
Lrrc4c	A	C	2: 97,459,391 (GRCm39)	T6P	probably benign	Het
Lrrk2	T	C	15: 91,626,469 (GRCm39)	L1171S	possibly damaging	Het
Man2b2	A	T	5: 36,978,378 (GRCm39)	M302K	probably damaging	Het
Mocos	G	A	18: 24,834,542 (GRCm39)	G860R	possibly damaging	Het
Mylk3	T	A	8: 86,085,571 (GRCm39)	D258V	possibly damaging	Het
Nkx1-2	C	T	7: 132,201,240 (GRCm39)	D6N	probably damaging	Het
Nrp2	A	G	1: 62,758,176 (GRCm39)	N54S	possibly damaging	Het
Nt5el	T	C	13: 105,256,473 (GRCm39)	I514T	possibly damaging	Het
Or2d2	A	G	7: 106,727,848 (GRCm39)	F251L	probably benign	Het
Pacsin1	A	T	17: 27,926,879 (GRCm39)	T195S	probably benign	Het
Pank4	T	C	4: 155,056,693 (GRCm39)		probably null	Het
Pdgfra	A	T	5: 75,327,180 (GRCm39)	M126L	probably benign	Het
Podxl	T	A	6: 31,505,432 (GRCm39)	T204S	probably benign	Het
Pole	G	A	5: 110,484,240 (GRCm39)	D2175N	probably damaging	Het
Pramel16	C	T	4: 143,677,267 (GRCm39)	G104E	probably benign	Het
Prkdc	A	G	16: 15,587,749 (GRCm39)	K2545E	probably benign	Het
Prodh	T	C	16: 17,897,849 (GRCm39)	I183V	probably benign	Het
Ptch1	T	C	13: 63,691,422 (GRCm39)	D277G	possibly damaging	Het
Rapgef5	G	A	12: 117,684,988 (GRCm39)	V246M	probably damaging	Het
Rubcnl	A	G	14: 75,269,834 (GRCm39)	N164S	probably benign	Het
Samd4	A	T	14: 47,290,419 (GRCm39)	L175F	probably damaging	Het
Scart1	G	A	7: 139,808,642 (GRCm39)	G851D	probably damaging	Het
Scimp	C	A	11: 70,688,893 (GRCm39)	W41L	possibly damaging	Het
Scn3a	T	A	2: 65,291,843 (GRCm39)	K1634N	possibly damaging	Het
Spta1	A	G	1: 174,030,888 (GRCm39)	R957G	probably benign	Het
Srebf1	T	C	11: 60,094,361 (GRCm39)	N609D	probably null	Het
Styxl1	A	T	5: 135,776,664 (GRCm39)	L164H	probably benign	Het
Synpo2l	A	T	14: 20,710,702 (GRCm39)	D865E	probably damaging	Het
Tnfsf15	T	C	4: 63,663,267 (GRCm39)	M19V	probably damaging	Het
Trappc8	G	C	18: 20,970,132 (GRCm39)	R953G	probably benign	Het
Trav13-1	A	G	14: 53,782,800 (GRCm39)	N50S	probably benign	Het
Trim12a	T	C	7: 103,955,241 (GRCm39)	K161E	probably benign	Het
Vipr1	C	A	9: 121,493,640 (GRCm39)	N230K	probably damaging	Het
Xirp1	A	T	9: 119,847,557 (GRCm39)	V3E	probably damaging	Het
Zfp768	A	G	7: 126,943,892 (GRCm39)	F82L	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
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
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'- CTAACCTGGACTCTGCAAAGCG -3'
(R):5'- GCCATTTGTACGCATGTGTG -3'

Sequencing Primer
(F):5'- ACTCTGCAAAGCGGACCG -3'
(R):5'- CGCATGTGTGTATTTATAGCAAAGG -3'

Posted On

2018-05-04