Mutagenetix > Incidental Mutation

Incidental Mutation 'R0055:Slc15a3'

152893

Institutional Source

Beutler Lab

Gene Symbol

Slc15a3

Ensembl Gene

ENSMUSG00000024737

Gene Name

solute carrier family 15, member 3

Synonyms

Ci1, cI-1

MMRRC Submission

038349-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0055 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

10819908-10835279 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to T at 10820406 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Stop codon at position 8 (E8*)

Ref Sequence

ENSEMBL: ENSMUSP00000025646 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025646]

AlphaFold

Q8BPX9

Predicted Effect

probably null
Transcript: ENSMUST00000025646
AA Change: E8*

SMART Domains

Protein: ENSMUSP00000025646
Gene: ENSMUSG00000024737
AA Change: E8*

Domain	Start	End	E-Value	Type
low complexity region	21	37	N/A	INTRINSIC
Pfam:MFS_1	38	508	3.4e-10	PFAM
Pfam:PTR2	101	519	3.2e-79	PFAM
transmembrane domain	538	557	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131010

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138263

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138380

Meta Mutation Damage Score

0.9572

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.6%
20x: 95.6%

Validation Efficiency

98% (59/60)

MGI Phenotype

PHENOTYPE: The gene is involved in pathogen sensing by dendritic cells. Homozygous KO results in a reduction of the number of these cells displaying tubular endo-lysosomes after LPS treatment. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	T	C	6: 128,547,057 (GRCm39)		probably benign	Het
Atp6v1h	A	T	1: 5,154,677 (GRCm39)	T2S	probably benign	Het
Bcl11b	G	A	12: 107,932,036 (GRCm39)	P179S	probably benign	Het
Cacna1a	C	T	8: 85,306,687 (GRCm39)		probably benign	Het
Ccdc146	C	T	5: 21,502,004 (GRCm39)		probably null	Het
Ccdc61	T	C	7: 18,626,461 (GRCm39)	D128G	probably damaging	Het
Cd55	A	G	1: 130,387,313 (GRCm39)		probably benign	Het
Cdk7	C	A	13: 100,855,812 (GRCm39)	E99*	probably null	Het
Cfap96	A	T	8: 46,421,198 (GRCm39)	S108R	probably damaging	Het
Cox8a	A	T	19: 7,194,874 (GRCm39)	S2T	probably damaging	Het
Cracdl	A	C	1: 37,663,337 (GRCm39)	S854A	probably benign	Het
Dennd5a	A	G	7: 109,498,998 (GRCm39)	I955T	possibly damaging	Het
Dop1a	A	C	9: 86,394,705 (GRCm39)	E602A	probably benign	Het
Ephx4	T	C	5: 107,560,944 (GRCm39)	L32S	probably damaging	Het
Fbxo21	T	A	5: 118,138,555 (GRCm39)	D493E	probably benign	Het
Frmd4b	A	T	6: 97,300,610 (GRCm39)		probably benign	Het
Fzd1	A	T	5: 4,806,037 (GRCm39)	M515K	possibly damaging	Het
Gli2	A	G	1: 118,818,138 (GRCm39)		probably benign	Het
Gm12887	T	A	4: 121,473,666 (GRCm39)	K61N	probably damaging	Het
Grin2a	A	T	16: 9,487,671 (GRCm39)	V409D	probably damaging	Het
Grin2b	T	C	6: 135,900,201 (GRCm39)	I227V	probably benign	Het
Helz2	T	G	2: 180,870,614 (GRCm39)	D2879A	possibly damaging	Het
Itpr2	T	C	6: 146,224,631 (GRCm39)	N1453S	probably benign	Het
Itpr3	C	A	17: 27,317,296 (GRCm39)	S817Y	probably damaging	Het
Lin7c	T	A	2: 109,726,798 (GRCm39)		probably benign	Het
Ly75	T	C	2: 60,152,262 (GRCm39)	E1097G	probably benign	Het
Mcm10	T	C	2: 4,996,218 (GRCm39)	N882D	probably damaging	Het
Mettl13	A	T	1: 162,373,750 (GRCm39)	L167Q	probably damaging	Het
Morn2	A	T	17: 80,602,942 (GRCm39)	M1L	probably benign	Het
Mybph	G	T	1: 134,121,590 (GRCm39)	V88L	probably damaging	Het
Nefm	T	A	14: 68,358,648 (GRCm39)		probably benign	Het
Nf1	A	G	11: 79,362,377 (GRCm39)	E1497G	probably damaging	Het
Or2j3	T	C	17: 38,615,702 (GRCm39)	S217G	possibly damaging	Het
Or4k37	T	A	2: 111,158,870 (GRCm39)	Y35*	probably null	Het
Or51ah3	A	G	7: 103,210,244 (GRCm39)	K187E	probably damaging	Het
Or52e18	T	A	7: 104,609,703 (GRCm39)	T79S	possibly damaging	Het
Phf8-ps	A	T	17: 33,285,696 (GRCm39)	W369R	probably damaging	Het
Plcd3	C	G	11: 102,968,411 (GRCm39)	W382S	probably damaging	Het
Plxna1	T	A	6: 89,306,721 (GRCm39)	I1370F	possibly damaging	Het
Qng1	T	C	13: 58,531,980 (GRCm39)	D192G	probably damaging	Het
Rarb	G	A	14: 16,509,066 (GRCm38)	R106C	probably damaging	Het
Rps6ka5	G	A	12: 100,644,839 (GRCm39)	T37I	probably damaging	Het
Runx1	G	T	16: 92,441,029 (GRCm39)		probably benign	Het
Scube1	A	G	15: 83,518,937 (GRCm39)	V301A	probably damaging	Het
Sema3a	A	T	5: 13,450,004 (GRCm39)	N27I	possibly damaging	Het
Slc22a5	T	C	11: 53,782,032 (GRCm39)	S112G	probably benign	Het
Slc25a45	T	C	19: 5,930,495 (GRCm39)	F3L	probably damaging	Het
Slc4a4	A	C	5: 89,304,195 (GRCm39)	H502P	possibly damaging	Het
Slfn10-ps	A	G	11: 82,921,126 (GRCm39)		noncoding transcript	Het
Slit2	C	A	5: 48,439,068 (GRCm39)	C1077*	probably null	Het
Spn	A	G	7: 126,735,494 (GRCm39)	F82L	possibly damaging	Het
Tbccd1	A	G	16: 22,660,655 (GRCm39)	W54R	probably damaging	Het
Ucp1	G	T	8: 84,017,233 (GRCm39)	E8*	probably null	Het
Unc80	A	T	1: 66,545,782 (GRCm39)		probably benign	Het
Vsnl1	A	T	12: 11,436,987 (GRCm39)		probably null	Het
Zdhhc11	C	T	13: 74,130,805 (GRCm39)	Q295*	probably null	Het
Zfp457	T	A	13: 67,442,098 (GRCm39)	H63L	probably damaging	Het

Other mutations in Slc15a3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00843:Slc15a3	APN	19	10,830,627 (GRCm39)	missense	probably null	0.60
IGL01131:Slc15a3	APN	19	10,834,986 (GRCm39)	unclassified	probably benign
IGL02098:Slc15a3	APN	19	10,826,042 (GRCm39)	missense	probably damaging	1.00
IGL02470:Slc15a3	APN	19	10,830,534 (GRCm39)	missense	probably benign
IGL03078:Slc15a3	APN	19	10,834,609 (GRCm39)	missense	probably damaging	0.99
IGL03197:Slc15a3	APN	19	10,832,443 (GRCm39)	critical splice donor site	probably null
R0019:Slc15a3	UTSW	19	10,833,404 (GRCm39)	missense	probably damaging	1.00
R0127:Slc15a3	UTSW	19	10,833,350 (GRCm39)	missense	probably damaging	0.99
R0133:Slc15a3	UTSW	19	10,820,614 (GRCm39)	missense	probably damaging	1.00
R1079:Slc15a3	UTSW	19	10,833,344 (GRCm39)	missense	probably benign	0.02
R1595:Slc15a3	UTSW	19	10,831,675 (GRCm39)	missense	probably benign
R1644:Slc15a3	UTSW	19	10,834,595 (GRCm39)	missense	possibly damaging	0.79
R1912:Slc15a3	UTSW	19	10,825,977 (GRCm39)	missense	probably damaging	1.00
R2074:Slc15a3	UTSW	19	10,834,663 (GRCm39)	missense	probably damaging	1.00
R2397:Slc15a3	UTSW	19	10,820,407 (GRCm39)	missense	probably benign
R4758:Slc15a3	UTSW	19	10,831,726 (GRCm39)	critical splice donor site	probably null
R4948:Slc15a3	UTSW	19	10,820,410 (GRCm39)	missense	probably benign	0.09
R5138:Slc15a3	UTSW	19	10,833,369 (GRCm39)	missense	probably damaging	1.00
R5319:Slc15a3	UTSW	19	10,833,296 (GRCm39)	missense	probably damaging	1.00
R5646:Slc15a3	UTSW	19	10,820,574 (GRCm39)	missense	probably benign	0.19
R6145:Slc15a3	UTSW	19	10,834,615 (GRCm39)	missense	probably damaging	1.00
R6606:Slc15a3	UTSW	19	10,826,046 (GRCm39)	missense	possibly damaging	0.91
R9038:Slc15a3	UTSW	19	10,820,866 (GRCm39)	missense	probably damaging	1.00
R9075:Slc15a3	UTSW	19	10,826,094 (GRCm39)	missense	probably damaging	1.00
R9639:Slc15a3	UTSW	19	10,820,717 (GRCm39)	nonsense	probably null
Z1176:Slc15a3	UTSW	19	10,825,922 (GRCm39)	missense	probably null	1.00

Predicted Primers

PCR Primer
(F):5'- TCCTAAATACCGGGTGACGTAGGC -3'
(R):5'- TTCAAGCTGTTGAGGTAGAGCACG -3'

Sequencing Primer
(F):5'- CATTGAGGCCCAGGTATCATAAG -3'
(R):5'- CACGAGGTTGGAGGTGACAC -3'

Genotyping

Genotyping is performed by amplifying the region containing the mutation using PCR, followed by sequencing of the amplified region to detect the mutation.

PCR Primers

R00550060_PCR_F: 5’- TCCTAAATACCGGGTGACGTAGGC-3’

R00550060_PCR_R: 5’- TTCAAGCTGTTGAGGTAGAGCACG-3’

Sequencing Primers

R00550060_SEQ_F: 5’- CATTGAGGCCCAGGTATCATAAG-3’ 

R00550060_SEQ_R: 5’- CACGAGGTTGGAGGTGACAC-3’ 

PCR program

1) 94°C 2:00

2) 94°C 0:30

3) 55°C 0:30

4) 72°C 1:00

5) repeat steps (2-4) 40X

6) 72°C 10:00

7) 4°C hold

The following sequence of 763 nucleotides is amplified:

tcctaaatac cgggtgacgt aggcagccac agggccagta aaaaggggaa gcccagggtt

tcttaagaag cagaaaaagg gacagaggct aagctgagag gaagagccag aggggactaa

ggaaggaaga gaagcagtca agcaaaaagg agtgtgtaga ggaggtggcc gggccagggg

agacattgag gcccaggtat cataagagaa ggggacaatt agaaaaggca gttaaccggg

gacactagag gaaagggggg ccgggaggat aaggtagtgg agcaagcagg atgatggggt

agggttgggg gggggggggt agactaggcc agagcagagg aaggaaagga gacgatttga

tagaagcaca ggggagatga acaagaagaa ctgggagggg aaggagtgag tggagagttc

aagtggagat agaaactagg tagcaaggag agggacctga gggaaaaaga gagagagaac

gacacggggt gagaaaagag ggcgatcagg gttaggggag aggaggggag gacagaggag

agagtctggg tcacggagac aggaaggcca ggatgtctgc ccctcgcgcg gaagagcaac

caagcaggtc cggagagcga caaccgctgg tggcccgagg cccgcgggga ccacgacggt

ggagacggac agctgctgct gcggtgctgc tagtgcagat gctggaacgc gctgccttct

ttggtgtcac ctccaacctc gtgctctacc tcaacagctt gaa

Primer binding sites are underlined and the sequencing primer is highlighted; the mutated nucleotide is shown in red text (Chr. (+) = G>T).

Posted On

2014-01-31