Mutagenetix > Incidental Mutation

Incidental Mutation 'R9085:Sptlc2'

690553

Institutional Source

Beutler Lab

Gene Symbol

Sptlc2

Ensembl Gene

ENSMUSG00000021036

Gene Name

serine palmitoyltransferase, long chain base subunit 2

Synonyms

LCB2, Spt2

MMRRC Submission

068904-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9085 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

87351832-87435129 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 87382839 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamic Acid at position 422 (K422E)

Ref Sequence

ENSEMBL: ENSMUSP00000021424 (fasta)

Gene Model

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

AlphaFold

P97363

Predicted Effect

probably benign
Transcript: ENSMUST00000021424
AA Change: K422E

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
AA Change: K422E

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (72/72)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Afg1l	G	A	10: 42,194,637 (GRCm39)	T385M	probably damaging	Het
Arhgap29	T	A	3: 121,808,249 (GRCm39)	D1142E	probably benign	Het
Ash1l	C	T	3: 88,889,294 (GRCm39)	A391V	probably benign	Het
Ash1l	T	C	3: 88,891,529 (GRCm39)	V1136A	probably benign	Het
Cacna1c	G	T	6: 118,615,466 (GRCm39)	Y1308*	probably null	Het
Cacna1g	A	T	11: 94,334,046 (GRCm39)	V865E	probably benign	Het
Cbx2	C	T	11: 118,919,914 (GRCm39)	T493M	possibly damaging	Het
Cyp2a12	T	C	7: 26,735,944 (GRCm39)	F451S	probably damaging	Het
Dlec1	G	T	9: 118,953,252 (GRCm39)	C572F	probably damaging	Het
Dmtn	A	G	14: 70,853,534 (GRCm39)	S92P	probably damaging	Het
Dnah10	T	C	5: 124,839,237 (GRCm39)	L1225P		Het
Dnah2	G	T	11: 69,320,224 (GRCm39)	H3954Q	possibly damaging	Het
Dntt	C	T	19: 41,044,220 (GRCm39)	R462C	probably damaging	Het
Emc1	T	C	4: 139,094,474 (GRCm39)	Y676H	possibly damaging	Het
Epb41l4b	A	T	4: 57,041,064 (GRCm39)		probably null	Het
Fer	T	A	17: 64,228,767 (GRCm39)	M214K	probably damaging	Het
Fgf17	A	G	14: 70,874,436 (GRCm39)	F129L	probably damaging	Het
Foxn3	C	T	12: 99,355,095 (GRCm39)	S23N	probably damaging	Het
Frmd4b	A	C	6: 97,269,334 (GRCm39)	S993A	probably benign	Het
Gdap1l1	T	C	2: 163,280,508 (GRCm39)	W15R	probably damaging	Het
Golga5	T	A	12: 102,458,476 (GRCm39)	S640T	probably benign	Het
Gucy2g	A	T	19: 55,221,597 (GRCm39)	Y301*	probably null	Het
Il31ra	T	C	13: 112,660,628 (GRCm39)	S654G		Het
Lmnb2	T	C	10: 80,740,091 (GRCm39)	D442G	probably benign	Het
Lpin1	T	C	12: 16,623,715 (GRCm39)	Y223C		Het
Lrrc37	A	G	11: 103,507,565 (GRCm39)	Y1468H	unknown	Het
Mast3	A	T	8: 71,249,361 (GRCm39)	W53R	unknown	Het
Mettl2	T	C	11: 105,021,274 (GRCm39)	V180A	possibly damaging	Het
Mospd3	C	T	5: 137,598,870 (GRCm39)		probably benign	Het
Mrpl18	A	T	17: 13,134,582 (GRCm39)	V61E	probably damaging	Het
Mrtfb	A	C	16: 13,230,092 (GRCm39)	T926P	probably damaging	Het
Muc2	T	A	7: 141,287,058 (GRCm39)	C154S	probably damaging	Het
Mypn	T	G	10: 62,983,894 (GRCm39)		probably null	Het
Nelfb	C	T	2: 25,094,292 (GRCm39)	C357Y	probably damaging	Het
Nes	T	G	3: 87,887,069 (GRCm39)	V1776G	possibly damaging	Het
Nin	T	A	12: 70,076,786 (GRCm39)	R1797*	probably null	Het
Nxpe2	A	T	9: 48,250,872 (GRCm39)	I25K	probably benign	Het
Or4a39	A	G	2: 89,236,641 (GRCm39)	S261P	probably damaging	Het
Or5ak24	T	A	2: 85,260,619 (GRCm39)	T185S	probably benign	Het
Osbpl1a	T	C	18: 13,062,093 (GRCm39)	H60R	probably damaging	Het
Papss1	C	A	3: 131,324,817 (GRCm39)	H425N	probably damaging	Het
Pde4dip	T	C	3: 97,601,385 (GRCm39)	N2344S	probably benign	Het
Pde6c	G	A	19: 38,166,569 (GRCm39)	V704I	probably benign	Het
Pknox1	C	T	17: 31,822,229 (GRCm39)	T332M	possibly damaging	Het
Pla2r1	A	T	2: 60,255,791 (GRCm39)	V1251D	probably damaging	Het
Plch2	T	C	4: 155,084,976 (GRCm39)	D321G	probably damaging	Het
Plec	A	G	15: 76,057,275 (GRCm39)	S4221P	probably damaging	Het
Psg23	T	G	7: 18,348,660 (GRCm39)	N49T	possibly damaging	Het
Qrfpr	A	G	3: 36,276,099 (GRCm39)	F97S	probably damaging	Het
Rab3ip	G	A	10: 116,775,310 (GRCm39)	S16L	probably damaging	Het
Rbm43	A	G	2: 51,824,930 (GRCm39)		probably benign	Het
Rpgrip1l	T	C	8: 92,014,303 (GRCm39)	N314D	possibly damaging	Het
Rpn2	C	T	2: 157,125,567 (GRCm39)	T26I	possibly damaging	Het
Rsph6a	A	T	7: 18,799,250 (GRCm39)	N294Y	probably damaging	Het
Serpinb9h	T	C	13: 33,581,781 (GRCm39)	Y113H	probably damaging	Het
Sesn1	C	T	10: 41,686,835 (GRCm39)		probably benign	Het
Sh3d19	T	C	3: 86,033,992 (GRCm39)	Y782H	probably damaging	Het
Sh3rf1	C	A	8: 61,802,493 (GRCm39)	D275E	probably benign	Het
Siglecg	T	C	7: 43,061,049 (GRCm39)	V374A	probably benign	Het
Slc6a11	A	T	6: 114,202,808 (GRCm39)	I301F	probably damaging	Het
Spock1	A	T	13: 57,570,956 (GRCm39)	F348I	unknown	Het
Tas2r115	A	T	6: 132,714,327 (GRCm39)	V208E	probably benign	Het
Tmem132a	G	T	19: 10,843,835 (GRCm39)	Q174K	probably damaging	Het
Tmtc1	A	T	6: 148,237,749 (GRCm39)	Y338*	probably null	Het
Tnfaip1	G	T	11: 78,420,965 (GRCm39)	L32I	probably damaging	Het
Tox2	T	C	2: 163,067,481 (GRCm39)	C67R	probably benign	Het
Ube2o	C	T	11: 116,436,209 (GRCm39)	G311S	probably damaging	Het
Unc13d	AATGCCTCCCATGCC	AATGCCTCCCATGCCTCCCATGCC	11: 115,958,998 (GRCm39)		probably benign	Het
Vav3	C	T	3: 109,413,722 (GRCm39)	A220V	probably benign	Het
Xaf1	A	G	11: 72,197,419 (GRCm39)	K132E	probably benign	Het
Zeb1	T	C	18: 5,766,716 (GRCm39)	L409S	probably damaging	Het
Zfp51	T	A	17: 21,684,660 (GRCm39)	L425H	probably damaging	Het

Other mutations in Sptlc2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00757:Sptlc2	APN	12	87,415,842 (GRCm39)	missense	probably damaging	0.99
IGL02458:Sptlc2	APN	12	87,356,667 (GRCm39)	utr 3 prime	probably benign
IGL02734:Sptlc2	APN	12	87,402,444 (GRCm39)	missense	probably damaging	0.97
IGL03252:Sptlc2	APN	12	87,402,431 (GRCm39)	missense	probably benign	0.00
lopsided	UTSW	12	87,388,339 (GRCm39)	missense	probably benign	0.27
shinola	UTSW	12	87,397,069 (GRCm39)	missense	possibly damaging	0.64
R0087:Sptlc2	UTSW	12	87,415,892 (GRCm39)	missense	probably benign
R0116:Sptlc2	UTSW	12	87,403,454 (GRCm39)	missense	probably benign	0.00
R0492:Sptlc2	UTSW	12	87,393,580 (GRCm39)	splice site	probably null
R1353:Sptlc2	UTSW	12	87,388,520 (GRCm39)	missense	probably damaging	1.00
R1470:Sptlc2	UTSW	12	87,402,414 (GRCm39)	missense	probably benign	0.00
R1470:Sptlc2	UTSW	12	87,402,414 (GRCm39)	missense	probably benign	0.00
R3417:Sptlc2	UTSW	12	87,393,582 (GRCm39)	splice site	probably benign
R3735:Sptlc2	UTSW	12	87,388,339 (GRCm39)	missense	probably benign	0.27
R3736:Sptlc2	UTSW	12	87,388,339 (GRCm39)	missense	probably benign	0.27
R4278:Sptlc2	UTSW	12	87,382,925 (GRCm39)	missense	probably benign	0.04
R5252:Sptlc2	UTSW	12	87,382,829 (GRCm39)	missense	possibly damaging	0.49
R5593:Sptlc2	UTSW	12	87,415,857 (GRCm39)	missense	probably benign	0.11
R5656:Sptlc2	UTSW	12	87,393,535 (GRCm39)	missense	probably damaging	1.00
R5801:Sptlc2	UTSW	12	87,388,545 (GRCm39)	splice site	probably null
R6256:Sptlc2	UTSW	12	87,402,305 (GRCm39)	missense	probably damaging	1.00
R6280:Sptlc2	UTSW	12	87,434,905 (GRCm39)	missense	probably benign
R6520:Sptlc2	UTSW	12	87,402,436 (GRCm39)	missense	probably benign
R6808:Sptlc2	UTSW	12	87,397,069 (GRCm39)	missense	possibly damaging	0.64
R7133:Sptlc2	UTSW	12	87,397,151 (GRCm39)	missense	probably benign	0.00
R7274:Sptlc2	UTSW	12	87,388,380 (GRCm39)	missense	probably benign	0.24
R7366:Sptlc2	UTSW	12	87,360,823 (GRCm39)	critical splice donor site	probably null
R7602:Sptlc2	UTSW	12	87,388,463 (GRCm39)	missense	probably damaging	0.99
R9710:Sptlc2	UTSW	12	87,359,533 (GRCm39)	missense	probably benign	0.44
Z1177:Sptlc2	UTSW	12	87,415,818 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- GGGAGCCAGTATAGTTATCAAAGTG -3'
(R):5'- ACCTTGAGTCCCAGCTTAGC -3'

Sequencing Primer
(F):5'- AAGCATATGTGGCCAGTG -3'
(R):5'- TGAGTCCCAGCTTAGCACCTG -3'

Posted On

2021-12-30