Mutagenetix > Incidental Mutation

Incidental Mutation 'R5656:Sptlc2'

442345

Institutional Source

Beutler Lab

Gene Symbol

Sptlc2

Ensembl Gene

ENSMUSG00000021036

Gene Name

serine palmitoyltransferase, long chain base subunit 2

Synonyms

LCB2

MMRRC Submission

043302-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5656 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

87305058-87388355 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 87346761 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 264 (L264Q)

Ref Sequence

ENSEMBL: ENSMUSP00000021424 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021424]

AlphaFold

P97363

Predicted Effect

probably damaging
Transcript: ENSMUST00000021424
AA Change: L264Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
AA Change: L264Q

Domain	Start	End	E-Value	Type
Pfam:Aminotran_1_2	166	526	7.2e-60	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167911

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169845

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170110

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.9%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a long chain base subunit of serine palmitoyltransferase. The enzyme, serine palmitoyltransferase, consists of two different subunits, and is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. A mutant allele of this gene in mice is used as a model for the human disease 'Susceptibilty to Psoriasis 1'. Mutations in the human gene are associated with hereditary sensory neuropathy type I. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality. Mice heterozygous for this allele exhibit abnormal liver and circulating shingolipid levels. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933405L10Rik	A	G	8: 105,709,512 (GRCm38)	S139G	probably benign	Het
Adrb3	T	C	8: 27,227,377 (GRCm38)	D348G	probably damaging	Het
Atg2b	A	G	12: 105,621,328 (GRCm38)	V1959A	probably benign	Het
Bicral	G	A	17: 46,808,369 (GRCm38)	T742M	probably damaging	Het
Bub1b	T	A	2: 118,605,431 (GRCm38)	I60N	probably damaging	Het
Ccdc162	A	G	10: 41,569,934 (GRCm38)	V414A	probably benign	Het
Cd22	T	G	7: 30,869,773 (GRCm38)	Y612S	probably damaging	Het
Cd68	T	A	11: 69,664,421 (GRCm38)	I320F	probably damaging	Het
Clca3a2	A	T	3: 144,797,632 (GRCm38)	N852K	probably benign	Het
Cpa6	T	A	1: 10,329,514 (GRCm38)	H363L	probably benign	Het
Ddx18	A	T	1: 121,561,358 (GRCm38)	L320Q	probably damaging	Het
Dnah5	A	G	15: 28,421,064 (GRCm38)	D3849G	probably benign	Het
Eci1	T	A	17: 24,437,309 (GRCm38)	N164K	probably damaging	Het
Efs	T	C	14: 54,917,127 (GRCm38)	T552A	probably damaging	Het
Fbp1	C	A	13: 62,875,196 (GRCm38)	V96L	probably damaging	Het
Gtf3c1	T	A	7: 125,662,654 (GRCm38)	N1139I	probably benign	Het
Gucy1b2	T	C	14: 62,422,981 (GRCm38)	Y152C	probably damaging	Het
Gxylt1	A	T	15: 93,245,661 (GRCm38)	L362Q	probably damaging	Het
Iqcd	A	G	5: 120,605,126 (GRCm38)		probably null	Het
Klhl41	T	A	2: 69,683,532 (GRCm38)	I585N	possibly damaging	Het
Map6	A	G	7: 99,336,298 (GRCm38)	K470E	probably damaging	Het
Mast3	T	C	8: 70,786,221 (GRCm38)	T496A	probably damaging	Het
Mbd6	A	T	10: 127,285,286 (GRCm38)		probably benign	Het
Melk	A	G	4: 44,312,237 (GRCm38)	K183R	possibly damaging	Het
Mta1	T	C	12: 113,123,139 (GRCm38)	V152A	probably damaging	Het
Naa35	G	A	13: 59,622,866 (GRCm38)		probably benign	Het
Nav3	A	C	10: 109,764,633 (GRCm38)	S1378A	probably damaging	Het
Ncapd3	T	A	9: 27,051,645 (GRCm38)	D415E	possibly damaging	Het
Nlrp4f	G	A	13: 65,190,871 (GRCm38)	R651*	probably null	Het
Or1e1f	T	A	11: 73,964,710 (GRCm38)	M34K	probably damaging	Het
Or5b121	A	G	19: 13,530,380 (GRCm38)	T280A	probably benign	Het
Or5p72	A	G	7: 108,422,618 (GRCm38)	I16V	probably benign	Het
P2rx7	A	T	5: 122,673,717 (GRCm38)	R364W	probably damaging	Het
Phactr2	T	C	10: 13,388,703 (GRCm38)	D2G	probably benign	Het
Phc3	G	T	3: 30,965,866 (GRCm38)	S28R	probably damaging	Het
Ppfia1	A	T	7: 144,519,974 (GRCm38)		probably null	Het
Prdm10	C	T	9: 31,353,417 (GRCm38)	T667M	probably benign	Het
Pwwp2b	T	A	7: 139,255,971 (GRCm38)	S443T	possibly damaging	Het
Pzp	T	C	6: 128,490,072 (GRCm38)	T1113A	probably damaging	Het
Rapgef6	A	G	11: 54,636,136 (GRCm38)	E551G	possibly damaging	Het
Sec23ip	A	G	7: 128,776,784 (GRCm38)	Y774C	probably damaging	Het
Setdb2	T	C	14: 59,419,118 (GRCm38)	D266G	probably damaging	Het
Shank1	T	C	7: 44,352,886 (GRCm38)	V1343A	probably benign	Het
Slf2	T	A	19: 44,973,235 (GRCm38)	D1064E	probably benign	Het
Slu7	A	G	11: 43,443,418 (GRCm38)	K424E	probably benign	Het
Smg1	A	T	7: 118,154,664 (GRCm38)		probably benign	Het
Sra1	A	G	18: 36,678,407 (GRCm38)	S93P	probably damaging	Het
Sult1c1	T	C	17: 53,964,652 (GRCm38)	E169G	probably benign	Het
Sv2a	A	G	3: 96,185,572 (GRCm38)	D196G	probably damaging	Het
Tbc1d22b	A	G	17: 29,594,780 (GRCm38)	I362M	probably damaging	Het
Tenm3	T	C	8: 48,228,762 (GRCm38)	D2611G	probably damaging	Het
Tmem43	T	C	6: 91,480,708 (GRCm38)	F191L	probably benign	Het
Trbv13-2	T	A	6: 41,121,694 (GRCm38)	Y68N	probably benign	Het
Ttn	T	G	2: 76,774,654 (GRCm38)	D18312A	possibly damaging	Het
Ublcp1	A	G	11: 44,465,606 (GRCm38)	V95A	probably damaging	Het
Usp17ld	A	G	7: 103,250,840 (GRCm38)	V295A	probably damaging	Het
Vmn1r29	T	A	6: 58,308,167 (GRCm38)	L291M	possibly damaging	Het
Vsig10l	C	T	7: 43,464,151 (GRCm38)	R176*	probably null	Het
Zbtb46	A	G	2: 181,423,417 (GRCm38)		probably null	Het
Zfp644	A	G	5: 106,637,982 (GRCm38)	V233A	probably benign	Het

Other mutations in Sptlc2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00757:Sptlc2	APN	12	87,369,068 (GRCm38)	missense	probably damaging	0.99
IGL02458:Sptlc2	APN	12	87,309,893 (GRCm38)	utr 3 prime	probably benign
IGL02734:Sptlc2	APN	12	87,355,670 (GRCm38)	missense	probably damaging	0.97
IGL03252:Sptlc2	APN	12	87,355,657 (GRCm38)	missense	probably benign	0.00
lopsided	UTSW	12	87,341,565 (GRCm38)	missense	probably benign	0.27
shinola	UTSW	12	87,350,295 (GRCm38)	missense	possibly damaging	0.64
R0087:Sptlc2	UTSW	12	87,369,118 (GRCm38)	missense	probably benign
R0116:Sptlc2	UTSW	12	87,356,680 (GRCm38)	missense	probably benign	0.00
R0492:Sptlc2	UTSW	12	87,346,806 (GRCm38)	splice site	probably null
R1353:Sptlc2	UTSW	12	87,341,746 (GRCm38)	missense	probably damaging	1.00
R1470:Sptlc2	UTSW	12	87,355,640 (GRCm38)	missense	probably benign	0.00
R1470:Sptlc2	UTSW	12	87,355,640 (GRCm38)	missense	probably benign	0.00
R3417:Sptlc2	UTSW	12	87,346,808 (GRCm38)	splice site	probably benign
R3735:Sptlc2	UTSW	12	87,341,565 (GRCm38)	missense	probably benign	0.27
R3736:Sptlc2	UTSW	12	87,341,565 (GRCm38)	missense	probably benign	0.27
R4278:Sptlc2	UTSW	12	87,336,151 (GRCm38)	missense	probably benign	0.04
R5252:Sptlc2	UTSW	12	87,336,055 (GRCm38)	missense	possibly damaging	0.49
R5593:Sptlc2	UTSW	12	87,369,083 (GRCm38)	missense	probably benign	0.11
R5801:Sptlc2	UTSW	12	87,341,771 (GRCm38)	splice site	probably null
R6256:Sptlc2	UTSW	12	87,355,531 (GRCm38)	missense	probably damaging	1.00
R6280:Sptlc2	UTSW	12	87,388,131 (GRCm38)	missense	probably benign
R6520:Sptlc2	UTSW	12	87,355,662 (GRCm38)	missense	probably benign
R6808:Sptlc2	UTSW	12	87,350,295 (GRCm38)	missense	possibly damaging	0.64
R7133:Sptlc2	UTSW	12	87,350,377 (GRCm38)	missense	probably benign	0.00
R7274:Sptlc2	UTSW	12	87,341,606 (GRCm38)	missense	probably benign	0.24
R7366:Sptlc2	UTSW	12	87,314,049 (GRCm38)	critical splice donor site	probably null
R7602:Sptlc2	UTSW	12	87,341,689 (GRCm38)	missense	probably damaging	0.99
R9085:Sptlc2	UTSW	12	87,336,065 (GRCm38)	missense	probably benign	0.00
R9710:Sptlc2	UTSW	12	87,312,759 (GRCm38)	missense	probably benign	0.44
Z1177:Sptlc2	UTSW	12	87,369,044 (GRCm38)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- TTAAAAGTCAAATCAAGGAAGACAGT -3'
(R):5'- TGGATAATTAAGTTGGCCAGGTGA -3'

Sequencing Primer
(F):5'- TTCGACCTCCCAAGTACTAGAATTG -3'
(R):5'- TTGGCCAGGTGAAGAAACTGTC -3'

Posted On

2016-11-09