Mutagenetix > Incidental Mutation

Incidental Mutation 'RF018:Sphk1'

603698

Institutional Source

Beutler Lab

Gene Symbol

Sphk1

Ensembl Gene

ENSMUSG00000061878

Gene Name

sphingosine kinase 1

Synonyms

1110006G24Rik, SK1

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

RF018 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

116421751-116427501 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 116425771 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 42 (S42T)

Ref Sequence

ENSEMBL: ENSMUSP00000131010 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000063396] [ENSMUST00000063446] [ENSMUST00000082152] [ENSMUST00000100201] [ENSMUST00000106386] [ENSMUST00000106387] [ENSMUST00000106388] [ENSMUST00000141798] [ENSMUST00000124682] [ENSMUST00000138840] [ENSMUST00000145737] [ENSMUST00000154034] [ENSMUST00000155102]

AlphaFold

Q8CI15

Predicted Effect

probably benign
Transcript: ENSMUST00000063396
AA Change: S36T

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000064743
Gene: ENSMUSG00000061878
AA Change: S36T

Domain	Start	End	E-Value	Type
DAGKc	16	153	1.19e-8	SMART
low complexity region	257	263	N/A	INTRINSIC
low complexity region	368	382	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000063446
AA Change: S36T

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000067865
Gene: ENSMUSG00000061878
AA Change: S36T

Domain	Start	End	E-Value	Type
DAGKc	16	153	1.19e-8	SMART
low complexity region	257	263	N/A	INTRINSIC
low complexity region	368	382	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000082152

SMART Domains

Protein: ENSMUSP00000080791
Gene: ENSMUSG00000020802

Domain	Start	End	E-Value	Type
low complexity region	2	47	N/A	INTRINSIC
low complexity region	79	110	N/A	INTRINSIC
low complexity region	289	298	N/A	INTRINSIC
low complexity region	379	391	N/A	INTRINSIC
low complexity region	470	505	N/A	INTRINSIC
low complexity region	516	528	N/A	INTRINSIC
low complexity region	705	712	N/A	INTRINSIC
low complexity region	715	737	N/A	INTRINSIC
coiled coil region	845	879	N/A	INTRINSIC
UBCc	953	1110	2.23e-16	SMART
Blast:UBCc	1201	1274	1e-15	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000100201
AA Change: S35T

PolyPhen 2 Score 0.125 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000097775
Gene: ENSMUSG00000061878
AA Change: S35T

Domain	Start	End	E-Value	Type
DAGKc	15	152	1.19e-8	SMART
low complexity region	256	262	N/A	INTRINSIC
low complexity region	367	381	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106386
AA Change: S36T

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000101994
Gene: ENSMUSG00000061878
AA Change: S36T

Domain	Start	End	E-Value	Type
DAGKc	16	153	1.19e-8	SMART
low complexity region	257	263	N/A	INTRINSIC
low complexity region	368	382	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106387
AA Change: S36T

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000101995
Gene: ENSMUSG00000061878
AA Change: S36T

Domain	Start	End	E-Value	Type
DAGKc	16	153	1.19e-8	SMART
low complexity region	257	263	N/A	INTRINSIC
low complexity region	368	382	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106388
AA Change: S36T

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000101996
Gene: ENSMUSG00000061878
AA Change: S36T

Domain	Start	End	E-Value	Type
DAGKc	16	153	1.19e-8	SMART
low complexity region	257	263	N/A	INTRINSIC
low complexity region	368	382	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000141798
AA Change: S42T

PolyPhen 2 Score 0.870 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000131010
Gene: ENSMUSG00000061878
AA Change: S42T

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
DAGKc	22	159	1.19e-8	SMART
low complexity region	263	269	N/A	INTRINSIC
low complexity region	374	388	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000124682
AA Change: S36T

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000116055
Gene: ENSMUSG00000061878
AA Change: S36T

Domain	Start	End	E-Value	Type
DAGKc	16	153	1.19e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000138840
AA Change: S35T

PolyPhen 2 Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000121064
Gene: ENSMUSG00000061878
AA Change: S35T

Domain	Start	End	E-Value	Type
DAGKc	15	152	1.19e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000145737
AA Change: S35T

PolyPhen 2 Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000114622
Gene: ENSMUSG00000061878
AA Change: S35T

Domain	Start	End	E-Value	Type
DAGKc	15	152	1.19e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000154034
AA Change: S35T

PolyPhen 2 Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000121219
Gene: ENSMUSG00000061878
AA Change: S35T

Domain	Start	End	E-Value	Type
DAGKc	15	152	1.19e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000155102
AA Change: S36T

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000114819
Gene: ENSMUSG00000061878
AA Change: S36T

Domain	Start	End	E-Value	Type
Pfam:DAGK_cat	16	116	4.6e-27	PFAM

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.3%
20x: 98.6%

Validation Efficiency

100% (54/54)

MGI Phenotype

FUNCTION: This gene encodes a kinase that phosphorylates sphingosine into sphingosine-1-phosphate, which is involved in cell differentiation, motility, and apoptosis. The encoded protein plays a role in maintaining cellular levels of sphingosine-1-phosphate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]
PHENOTYPE: Homozygous null mice are viable, fertile, and without any obvious abnormalities. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A030005L19Rik	GTGGCTGCT	GTGGCTGCTTTGGCTGCT	1: 82,891,293 (GRCm39)		probably benign	Het
Abca15	T	A	7: 119,993,683 (GRCm39)	V1301E	possibly damaging	Het
Adcy10	T	A	1: 165,379,678 (GRCm39)	V980E	probably damaging	Het
Aldh1a2	T	C	9: 71,192,552 (GRCm39)	V469A	probably damaging	Het
Alk	T	A	17: 72,256,808 (GRCm39)	T684S	probably benign	Het
Ankhd1	GGCGGC	GGCGGCAGCGGC	18: 36,693,965 (GRCm39)		probably benign	Het
Anks1b	G	A	10: 89,869,087 (GRCm39)	G49D	probably damaging	Het
Blm	CCTCCTCC	CCTCCTCCTCCTACTCCTCC	7: 80,162,674 (GRCm39)		probably null	Het
Btnl10	CAAA	CAAAAAA	11: 58,814,752 (GRCm39)		probably benign	Het
Ccdc81	C	A	7: 89,515,906 (GRCm39)		probably null	Het
Cd209g	A	G	8: 4,187,398 (GRCm39)	Y194C	probably benign	Het
Cenpc1	A	T	5: 86,193,228 (GRCm39)	S220R	possibly damaging	Het
Ddx42	A	T	11: 106,123,630 (GRCm39)		probably null	Het
Dock4	GTGCCGGTGCCCGT	G	12: 40,894,398 (GRCm39)		probably null	Het
Eif5b	A	T	1: 38,060,673 (GRCm39)		probably null	Het
Ell2	C	A	13: 75,911,727 (GRCm39)	H338N	probably damaging	Het
Entpd2	CTT	CTTT	2: 25,290,907 (GRCm39)		probably null	Het
Flywch1	CCACTCCTGGTGT	CCACTCCTGGTGTGGGGAGGCTACGTACTCACGCACTCCTGGTGT	17: 23,981,140 (GRCm39)		probably null	Het
Gm8369	GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	19: 11,489,106 (GRCm39)		probably null	Het
Gnat2	T	C	3: 108,003,645 (GRCm39)	S107P	unknown	Het
Guk1	T	A	11: 59,077,234 (GRCm39)	D70V	probably benign	Het
Itpkb	C	T	1: 180,160,887 (GRCm39)	R338W	probably damaging	Het
Krtap28-10	ACCACAGCCACAGCCACCACAGCCACAGCC	ACCACAGCCACAGCCCCCACAGCCACAGCCACCACAGCCACAGCC	1: 83,019,974 (GRCm39)		probably benign	Het
Lamp3	A	C	16: 19,520,000 (GRCm39)	I61R	probably benign	Het
Lrch1	GCTGGTGGTGT	G	14: 75,184,995 (GRCm39)		probably null	Het
Lrp1b	C	T	2: 41,000,919 (GRCm39)	E2216K		Het
Lrrc27	A	G	7: 138,806,016 (GRCm39)	D227G	probably benign	Het
Lrrk1	C	T	7: 66,031,250 (GRCm39)	G16E	possibly damaging	Het
Lrrtm1	T	A	6: 77,221,334 (GRCm39)	S264T	possibly damaging	Het
Lypd8	CCAATCACCAACA	CCAATCACCAACAGTTTCCTCGCCTCTGTTACCCCACCAATCACCAACA	11: 58,281,058 (GRCm39)		probably benign	Het
Mamld1	CAG	CAGAAG	X: 70,162,455 (GRCm39)		probably benign	Het
Mpo	G	C	11: 87,688,465 (GRCm39)	A375P	probably damaging	Het
Myo9a	A	G	9: 59,776,869 (GRCm39)	H1089R	probably benign	Het
Nalf2	CGCCGC	CGCCGCTGCCGC	X: 98,864,967 (GRCm39)		probably benign	Het
Ndufc2	T	C	7: 97,056,228 (GRCm39)	*109Q	probably null	Het
Nudt16	A	T	9: 105,008,898 (GRCm39)	Y28N	probably damaging	Het
Nudt4	A	T	10: 95,385,675 (GRCm39)		probably null	Het
Nusap1	AGATACACGTTAGCAGTGAGGAGCAAGCTG	AGATACACGTTAGCAGTGAGGAGCAAGCTGCGATACACGTTAGCAGTGAGGAGCAAGCTG	2: 119,458,059 (GRCm39)		probably benign	Het
Or2ag15	T	A	7: 106,340,692 (GRCm39)	I150F	probably benign	Het
P2ry12	T	A	3: 59,124,833 (GRCm39)	T281S	probably benign	Het
P4ha2	TGTTGG	T	11: 54,001,072 (GRCm39)		probably null	Het
Pcnx2	A	G	8: 126,604,258 (GRCm39)	V666A	probably damaging	Het
Pde6a	T	A	18: 61,364,475 (GRCm39)	I177N	possibly damaging	Het
Pgm1	A	T	4: 99,819,500 (GRCm39)		probably null	Het
Plce1	T	A	19: 38,705,651 (GRCm39)	W1019R	probably damaging	Het
Plch1	C	A	3: 63,628,636 (GRCm39)	K542N	probably damaging	Het
Plekhj1	T	C	10: 80,632,471 (GRCm39)	Q113R	not run	Het
Postn	A	T	3: 54,291,913 (GRCm39)	I705F	probably damaging	Het
Ppp1r15b	G	T	1: 133,059,352 (GRCm39)		probably benign	Het
Prkab1	T	C	5: 116,159,689 (GRCm39)	E59G	probably damaging	Het
Qrfprl	T	A	6: 65,433,174 (GRCm39)	Y331*	probably null	Het
Raph1	GG	GGGGG	1: 60,528,426 (GRCm39)		probably benign	Het
Rassf6	AGCAATGGGGATTC	AGCAATGGGGATTCTGCCTCACTCATGGTCCTGTAGCGCAATGGGGATTC	5: 90,756,788 (GRCm39)		probably benign	Het
Rnf144a	TCTC	TCTCTCTCTCTCTCTCACTC	12: 26,364,013 (GRCm39)		probably benign	Het
Ros1	T	A	10: 52,031,217 (GRCm39)	M484L	probably benign	Het
Rpa1	GCTGCTGCC	GC	11: 75,209,343 (GRCm39)		probably null	Het
Sectm1b	A	G	11: 120,945,756 (GRCm39)	V195A	probably benign	Het
Sirpa	TCATCAG	T	2: 129,451,123 (GRCm39)		probably null	Het
Slc28a1	T	A	7: 80,819,032 (GRCm39)		probably null	Het
Spta1	T	C	1: 174,036,885 (GRCm39)	L1132P	probably damaging	Het
Srrt	A	T	5: 137,298,262 (GRCm39)	N303K	probably benign	Het
Ssh2	A	G	11: 77,344,880 (GRCm39)	E955G	probably damaging	Het
Strn	CCAGTC	CCAGTCCGTGCTCCCTTACCCCAGTCCGTGCTCCCTTACCACAGTC	17: 78,984,712 (GRCm39)		probably null	Het
Tchhl1	T	C	3: 93,377,691 (GRCm39)	F132L	probably benign	Het
Tex14	A	G	11: 87,405,572 (GRCm39)	E828G	probably benign	Het
Tfeb	CAG	CAGGAG	17: 48,097,020 (GRCm39)		probably benign	Het
Tmtc1	T	C	6: 148,149,009 (GRCm39)	Y699C	probably damaging	Het
Ubn1	A	G	16: 4,882,256 (GRCm39)	Y239C	probably damaging	Het
Vmn2r23	T	G	6: 123,690,075 (GRCm39)	L317R	probably benign	Het
Vmn2r78	C	T	7: 86,603,639 (GRCm39)	R606*	probably null	Het
Vps72	T	G	3: 95,028,719 (GRCm39)		probably null	Het
Zc3h11a	A	G	1: 133,554,853 (GRCm39)	S376P	possibly damaging	Het
Zfp384	GCCCAGGC	GCCCAGGCCCAGTCCCAGGC	6: 125,013,452 (GRCm39)		probably benign	Het
Zfp598	CAACCAC	CAACCACAACCAC	17: 24,899,745 (GRCm39)		probably benign	Het
Zfp628	TACTCCTCCACCC	T	7: 4,923,948 (GRCm39)		probably benign	Het

Other mutations in Sphk1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
P0040:Sphk1	UTSW	11	116,425,891 (GRCm39)	splice site	probably benign
R0565:Sphk1	UTSW	11	116,427,184 (GRCm39)	unclassified	probably benign
R1307:Sphk1	UTSW	11	116,426,928 (GRCm39)	missense	probably benign	0.09
R1635:Sphk1	UTSW	11	116,426,596 (GRCm39)	missense	probably damaging	1.00
R1940:Sphk1	UTSW	11	116,426,676 (GRCm39)	missense	probably benign	0.00
R4685:Sphk1	UTSW	11	116,426,106 (GRCm39)	missense	probably damaging	1.00
R5440:Sphk1	UTSW	11	116,425,714 (GRCm39)	missense	possibly damaging	0.54
R5621:Sphk1	UTSW	11	116,427,192 (GRCm39)	unclassified	probably benign
R6767:Sphk1	UTSW	11	116,426,982 (GRCm39)	missense	possibly damaging	0.93
R7150:Sphk1	UTSW	11	116,425,907 (GRCm39)	missense	probably benign	0.07
R7207:Sphk1	UTSW	11	116,426,590 (GRCm39)	missense	probably damaging	1.00
R7758:Sphk1	UTSW	11	116,427,063 (GRCm39)	missense	possibly damaging	0.75
R8084:Sphk1	UTSW	11	116,425,904 (GRCm39)	critical splice acceptor site	probably null
R8733:Sphk1	UTSW	11	116,426,451 (GRCm39)	missense	probably benign	0.32
R8827:Sphk1	UTSW	11	116,426,590 (GRCm39)	missense	probably damaging	1.00
R9034:Sphk1	UTSW	11	116,426,449 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACTGGTTGTGGACATTACCATTC -3'
(R):5'- TCAGACCATCACCGGACATG -3'

Sequencing Primer
(F):5'- GAACTCACTCTGTAGACCAGGTTG -3'
(R):5'- TCACCGGACATGACTGCCAG -3'

Posted On

2019-12-04