Mutagenetix > Incidental Mutation

Incidental Mutation 'R4868:Sdf4'

376309

Institutional Source

Beutler Lab

Gene Symbol

Sdf4

Ensembl Gene

ENSMUSG00000029076

Gene Name

stromal cell derived factor 4

Synonyms

Cab45

MMRRC Submission

042478-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.143) question?

Stock #

R4868 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

156077329-156098067 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 156093642 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 259 (S259T)

Ref Sequence

ENSEMBL: ENSMUSP00000101204 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030952] [ENSMUST00000050078] [ENSMUST00000105578] [ENSMUST00000105579]

AlphaFold

Q61112

Predicted Effect

probably benign
Transcript: ENSMUST00000030952

SMART Domains

Protein: ENSMUSP00000030952
Gene: ENSMUSG00000029075

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
TNFR	27	60	6.24e-6	SMART
TNFR	63	103	1.33e-9	SMART
TNFR	126	164	2.59e-3	SMART
transmembrane domain	213	235	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000050078
AA Change: S259T

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

SMART Domains

Protein: ENSMUSP00000053175
Gene: ENSMUSG00000029076
AA Change: S259T

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC
low complexity region	44	54	N/A	INTRINSIC
EFh	101	129	7.93e-1	SMART
EFh	140	168	3.34e1	SMART
EFh	236	264	3.48e-1	SMART
EFh	284	309	4.08e1	SMART
EFh	317	345	2.9e1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000105578
AA Change: S259T

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

SMART Domains

Protein: ENSMUSP00000101203
Gene: ENSMUSG00000029076
AA Change: S259T

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC
low complexity region	44	54	N/A	INTRINSIC
EFh	101	129	7.93e-1	SMART
EFh	140	168	3.34e1	SMART
EFh	236	264	3.48e-1	SMART
EFh	284	309	4.08e1	SMART
EFh	317	345	2.9e1	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000105579
AA Change: S259T

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

SMART Domains

Protein: ENSMUSP00000101204
Gene: ENSMUSG00000029076
AA Change: S259T

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC
low complexity region	44	54	N/A	INTRINSIC
EFh	101	129	7.93e-1	SMART
EFh	140	168	3.34e1	SMART
EFh	236	264	3.48e-1	SMART
EFh	284	309	4.08e1	SMART
EFh	317	345	2.9e1	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143576

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149971

Meta Mutation Damage Score

0.3758

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.7%

Validation Efficiency

99% (91/92)

MGI Phenotype

FUNCTION: This gene encodes a member of the CREC family. The encoded protein contains multiple calcium-binding EF-hand motifs. This protein localizes to the Golgi lumen and may be involved in regulating calcium dependent cellular activities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933405L10Rik	A	G	8: 106,436,729 (GRCm39)	*299W	probably null	Het
4933412E24Rik	G	A	15: 59,887,817 (GRCm39)	L208F	possibly damaging	Het
Abca8b	G	A	11: 109,865,338 (GRCm39)	A373V	probably benign	Het
Actn3	A	T	19: 4,914,482 (GRCm39)	W549R	probably benign	Het
Adamts4	C	T	1: 171,080,000 (GRCm39)		probably benign	Het
Adcy4	T	C	14: 56,011,179 (GRCm39)	I615V	probably benign	Het
Akap1	A	G	11: 88,735,379 (GRCm39)	S428P	possibly damaging	Het
Akap13	A	T	7: 75,393,252 (GRCm39)	R2476W	probably damaging	Het
Alx3	A	G	3: 107,507,943 (GRCm39)	S151G	possibly damaging	Het
Aoah	T	A	13: 21,099,151 (GRCm39)	Y243*	probably null	Het
Asap1	A	G	15: 63,966,030 (GRCm39)	V1025A	probably benign	Het
Atp8b1	A	T	18: 64,684,937 (GRCm39)	I728N	probably damaging	Het
Baz2b	C	A	2: 59,755,226 (GRCm39)	V1001L	possibly damaging	Het
Bmpr2	T	A	1: 59,909,615 (GRCm39)	S1030T	probably benign	Het
Cacna2d3	A	T	14: 28,678,743 (GRCm39)		probably null	Het
Casp3	A	T	8: 47,087,314 (GRCm39)	N87I	probably benign	Het
Ccdc171	T	A	4: 83,612,569 (GRCm39)	L995Q	probably damaging	Het
Ccdc80	T	A	16: 44,924,776 (GRCm39)	Y637N	probably damaging	Het
Ccr4	A	G	9: 114,321,901 (GRCm39)	F55L	probably benign	Het
Cmah	T	A	13: 24,648,247 (GRCm39)	V494E	probably damaging	Het
Cnot6l	A	G	5: 96,230,882 (GRCm39)	Y362H	probably damaging	Het
Coq6	T	C	12: 84,417,726 (GRCm39)	V222A	probably damaging	Het
Ctdspl2	C	A	2: 121,823,879 (GRCm39)	T240N	possibly damaging	Het
D430041D05Rik	T	C	2: 104,085,754 (GRCm39)	T248A	possibly damaging	Het
Dctn6	A	T	8: 34,559,230 (GRCm39)		probably benign	Het
Dhx34	T	C	7: 15,933,727 (GRCm39)	D955G	probably benign	Het
Dnaaf5	A	G	5: 139,155,941 (GRCm39)	M541V	probably benign	Het
Dnah17	A	T	11: 117,999,038 (GRCm39)	S912T	probably benign	Het
Dnah2	A	T	11: 69,354,474 (GRCm39)	V2248E	probably damaging	Het
Dysf	T	C	6: 84,156,675 (GRCm39)	W1502R	probably damaging	Het
Dzip1	A	T	14: 119,114,626 (GRCm39)	V843E	probably damaging	Het
Esp23	G	T	17: 39,384,915 (GRCm39)	T27K	probably benign	Het
Esp3	A	T	17: 40,944,420 (GRCm39)	M21L	possibly damaging	Het
Fam43b	T	A	4: 138,123,108 (GRCm39)	T71S	probably benign	Het
Fpgs	G	A	2: 32,582,673 (GRCm39)	R63C	probably damaging	Het
H2-M11	G	T	17: 36,859,811 (GRCm39)	W268L	probably damaging	Het
Inpp5b	T	C	4: 124,645,203 (GRCm39)	S210P	probably damaging	Het
Itsn1	T	A	16: 91,582,205 (GRCm39)	S51T	probably damaging	Het
Kctd2	G	A	11: 115,320,205 (GRCm39)	V246I	probably damaging	Het
Krt75	C	T	15: 101,476,556 (GRCm39)	G403E	probably damaging	Het
Lamp3	T	A	16: 19,520,040 (GRCm39)	T48S	probably benign	Het
Lyzl4	C	A	9: 121,412,075 (GRCm39)	V114L	probably damaging	Het
Maml3	C	A	3: 52,011,345 (GRCm39)	E74*	probably null	Het
Map2k7	G	A	8: 4,297,751 (GRCm39)		probably benign	Het
Mapk8ip3	A	G	17: 25,120,389 (GRCm39)	V883A	probably benign	Het
Mbtps1	C	T	8: 120,235,667 (GRCm39)	V1004I	probably benign	Het
Metap1	G	T	3: 138,188,850 (GRCm39)	H48Q	probably damaging	Het
Mical2	T	A	7: 111,917,831 (GRCm39)	V396E	probably damaging	Het
Mks1	T	A	11: 87,744,549 (GRCm39)		probably benign	Het
Ndst1	T	C	18: 60,828,548 (GRCm39)	T669A	probably benign	Het
Obox3	T	C	7: 15,361,235 (GRCm39)	K10R	probably damaging	Het
Opn3	T	C	1: 175,491,127 (GRCm39)	Y302C	probably damaging	Het
Or4f62	T	A	2: 111,986,916 (GRCm39)	S207T	probably damaging	Het
Or6b6	C	T	7: 106,570,974 (GRCm39)	M192I	probably benign	Het
Or9g8	T	G	2: 85,606,970 (GRCm39)	V14G	possibly damaging	Het
Pdzph1	A	T	17: 59,281,751 (GRCm39)	V177D	probably benign	Het
Pex5l	T	A	3: 33,006,639 (GRCm39)	I577F	probably damaging	Het
Pmpcb	T	A	5: 21,953,851 (GRCm39)	Y366*	probably null	Het
Prr14l	A	T	5: 32,987,281 (GRCm39)	M738K	probably benign	Het
Prx	T	C	7: 27,217,004 (GRCm39)	S641P	probably benign	Het
Ptchd3	A	G	11: 121,721,883 (GRCm39)	Y252C	possibly damaging	Het
Reg3a	A	G	6: 78,358,883 (GRCm39)	E27G	probably damaging	Het
Ripor2	A	G	13: 24,878,124 (GRCm39)	T300A	possibly damaging	Het
Sike1	A	G	3: 102,904,730 (GRCm39)		probably null	Het
Sis	T	G	3: 72,850,881 (GRCm39)	I606L	probably benign	Het
Slc30a9	T	C	5: 67,482,026 (GRCm39)	I94T	probably benign	Het
Slc5a4a	T	C	10: 76,014,065 (GRCm39)	I424T	probably damaging	Het
Spx	C	T	6: 142,362,116 (GRCm39)	R72*	probably null	Het
St7	C	A	6: 17,819,265 (GRCm39)	N56K	probably damaging	Het
Tcte2	C	A	17: 13,948,270 (GRCm39)	G3V	probably damaging	Het
Tent5b	A	G	4: 133,213,393 (GRCm39)		probably null	Het
Tgfb3	T	C	12: 86,108,955 (GRCm39)	D258G	probably benign	Het
Timeless	G	T	10: 128,083,230 (GRCm39)	G659V	probably benign	Het
Tnn	T	C	1: 159,958,443 (GRCm39)	R467G	possibly damaging	Het
Tor1b	T	C	2: 30,846,589 (GRCm39)		probably null	Het
Trank1	T	A	9: 111,194,709 (GRCm39)	L911Q	probably damaging	Het
Ttll2	C	T	17: 7,618,998 (GRCm39)	V310I	probably benign	Het
Ttyh3	A	T	5: 140,615,221 (GRCm39)	I389N	probably damaging	Het
Tut4	T	C	4: 108,406,417 (GRCm39)		probably benign	Het
Ube3b	T	C	5: 114,536,488 (GRCm39)	V216A	probably benign	Het
Vezf1	T	A	11: 87,965,520 (GRCm39)	V254E	probably damaging	Het
Vmn1r122	T	C	7: 20,867,227 (GRCm39)	E276G	probably benign	Het
Vmn1r167	T	A	7: 23,204,161 (GRCm39)	N285I	probably benign	Het
Vmn2r45	T	A	7: 8,484,480 (GRCm39)	I442F	probably benign	Het
Vwa8	C	A	14: 79,420,522 (GRCm39)	A1741E	probably damaging	Het
Wdr20	T	A	12: 110,704,668 (GRCm39)	V69E	probably damaging	Het
Xkr4	T	G	1: 3,287,074 (GRCm39)	Q372P	probably damaging	Het

Other mutations in Sdf4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01161:Sdf4	APN	4	156,093,763 (GRCm39)	missense	probably benign	0.00
IGL02283:Sdf4	APN	4	156,093,293 (GRCm39)	missense	probably benign
IGL02666:Sdf4	APN	4	156,093,281 (GRCm39)	nonsense	probably null
IGL02893:Sdf4	APN	4	156,080,985 (GRCm39)	splice site	probably benign
IGL03246:Sdf4	APN	4	156,085,154 (GRCm39)	missense	probably benign	0.01
soap	UTSW	4	156,086,916 (GRCm39)	splice site	probably null
R1648:Sdf4	UTSW	4	156,083,886 (GRCm39)	missense	probably damaging	0.96
R1879:Sdf4	UTSW	4	156,094,304 (GRCm39)	missense	probably damaging	1.00
R1893:Sdf4	UTSW	4	156,085,205 (GRCm39)	missense	probably benign	0.22
R3793:Sdf4	UTSW	4	156,086,916 (GRCm39)	splice site	probably null
R4255:Sdf4	UTSW	4	156,085,214 (GRCm39)	missense	probably benign	0.00
R4436:Sdf4	UTSW	4	156,093,404 (GRCm39)	critical splice donor site	probably null
R4801:Sdf4	UTSW	4	156,085,178 (GRCm39)	missense	possibly damaging	0.66
R4802:Sdf4	UTSW	4	156,085,178 (GRCm39)	missense	possibly damaging	0.66
R5752:Sdf4	UTSW	4	156,080,761 (GRCm39)	missense	probably damaging	1.00
R5813:Sdf4	UTSW	4	156,083,856 (GRCm39)	missense	probably benign	0.03
R7501:Sdf4	UTSW	4	156,080,977 (GRCm39)	critical splice donor site	probably null
R8109:Sdf4	UTSW	4	156,094,295 (GRCm39)	missense	probably damaging	0.99
R8167:Sdf4	UTSW	4	156,093,379 (GRCm39)	missense	possibly damaging	0.95
R8867:Sdf4	UTSW	4	156,093,759 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGTGACACTGTTTTCGGCC -3'
(R):5'- TGTAGGATTAGCCGAGCCTC -3'

Sequencing Primer
(F):5'- TTTTCGGCCCGAGGGTAAC -3'
(R):5'- TAGGATTAGCCGAGCCTCCAAAC -3'

Posted On

2016-03-17