Mutagenetix > Incidental Mutation

Incidental Mutation 'R5813:Sdf4'

501534

Institutional Source

Beutler Lab

Gene Symbol

Sdf4

Ensembl Gene

ENSMUSG00000029076

Gene Name

stromal cell derived factor 4

Synonyms

Cab45

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.147) question?

Stock #

R5813 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

156077329-156098067 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 156083856 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 109 (V109I)

Ref Sequence

ENSEMBL: ENSMUSP00000101204 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000050078] [ENSMUST00000097734] [ENSMUST00000105578] [ENSMUST00000105579]

AlphaFold

Q61112

Predicted Effect

probably benign
Transcript: ENSMUST00000050078
AA Change: V109I

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000053175
Gene: ENSMUSG00000029076
AA Change: V109I

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 benign
Transcript: ENSMUST00000097734
AA Change: V109I

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000095340
Gene: ENSMUSG00000029076
AA Change: V109I

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

Predicted Effect

probably benign
Transcript: ENSMUST00000105578
AA Change: V109I

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000101203
Gene: ENSMUSG00000029076
AA Change: V109I

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 benign
Transcript: ENSMUST00000105579
AA Change: V109I

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000101204
Gene: ENSMUSG00000029076
AA Change: V109I

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: ENSMUST00000124872

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam15	A	G	3: 89,253,135 (GRCm39)	Y230H	probably benign	Het
Ano7	G	T	1: 93,312,641 (GRCm39)		probably null	Het
Arap2	T	C	5: 62,834,506 (GRCm39)	Y792C	probably damaging	Het
Art3	C	A	5: 92,560,100 (GRCm39)		probably benign	Het
Atad2	C	T	15: 57,963,250 (GRCm39)	G1085D	probably benign	Het
Birc6	C	A	17: 74,953,497 (GRCm39)	A3253E	probably damaging	Het
C9	C	T	15: 6,526,607 (GRCm39)	P547L	probably benign	Het
Cecr2	T	C	6: 120,739,169 (GRCm39)	S1271P	probably damaging	Het
Ces1e	T	A	8: 93,948,305 (GRCm39)	K105*	probably null	Het
Cpsf4	A	G	5: 145,115,683 (GRCm39)	N204S	probably benign	Het
Cracd	A	G	5: 77,006,275 (GRCm39)	T879A	unknown	Het
Dgkz	T	C	2: 91,769,733 (GRCm39)	D615G	possibly damaging	Het
Disp1	G	T	1: 182,869,974 (GRCm39)	N815K	probably damaging	Het
Enah	A	G	1: 181,758,750 (GRCm39)		probably benign	Het
Fcgbp	A	G	7: 27,800,919 (GRCm39)	T1322A	possibly damaging	Het
Frem1	A	G	4: 82,918,395 (GRCm39)	F516L	probably damaging	Het
Fry	G	A	5: 150,323,136 (GRCm39)	A1096T	probably damaging	Het
Fyco1	T	C	9: 123,660,413 (GRCm39)	Y190C	probably damaging	Het
Gfra1	T	C	19: 58,227,687 (GRCm39)	D417G	probably benign	Het
Gigyf2	T	C	1: 87,368,485 (GRCm39)	I1055T	probably damaging	Het
Invs	A	G	4: 48,398,146 (GRCm39)	E444G	probably damaging	Het
Itga10	A	G	3: 96,559,901 (GRCm39)	T519A	probably benign	Het
Itgb4	C	T	11: 115,874,983 (GRCm39)	R447W	probably benign	Het
Kdm2b	A	G	5: 123,009,931 (GRCm39)	S727P	probably benign	Het
Kidins220	A	T	12: 25,107,139 (GRCm39)	K1531*	probably null	Het
Ksr1	C	T	11: 78,929,024 (GRCm39)	V266M	probably damaging	Het
Lin9	T	A	1: 180,496,763 (GRCm39)	L351I	probably benign	Het
Lipi	T	C	16: 75,370,798 (GRCm39)	R140G	possibly damaging	Het
Lrrc32	T	C	7: 98,147,618 (GRCm39)	S133P	probably damaging	Het
Map3k7	T	A	4: 31,964,318 (GRCm39)	I19N	probably damaging	Het
Marf1	A	G	16: 13,970,449 (GRCm39)	V90A	probably benign	Het
Mark3	T	C	12: 111,621,877 (GRCm39)	L673P	probably damaging	Het
Meis1	T	C	11: 18,966,229 (GRCm39)	H48R	probably benign	Het
Mettl26	G	A	17: 26,094,995 (GRCm39)	V87M	probably damaging	Het
Mknk2	T	C	10: 80,511,696 (GRCm39)	R5G	probably benign	Het
Mtcl3	G	T	10: 29,026,240 (GRCm39)	V441F	probably damaging	Het
Mterf1b	T	C	5: 4,246,956 (GRCm39)	V199A	possibly damaging	Het
Ncs1	T	A	2: 31,170,666 (GRCm39)		probably null	Het
Nek10	T	C	14: 14,986,704 (GRCm38)	V1014A	probably benign	Het
Notch2	A	G	3: 98,042,744 (GRCm39)	N1370D	probably benign	Het
Nr2e3	TCCATCGGAGTGTTCCC	TC	9: 59,850,701 (GRCm39)		probably benign	Het
Opn5	C	G	17: 42,903,897 (GRCm39)	R146T	probably damaging	Het
Or1e16	AGCGGTCGTAGGC	AGC	11: 73,286,480 (GRCm39)		probably null	Het
Or5m3	T	C	2: 85,838,636 (GRCm39)	I172T	probably damaging	Het
Or8b55	T	A	9: 38,726,952 (GRCm39)	M51K	probably benign	Het
Or8g33	A	G	9: 39,338,032 (GRCm39)	C112R	probably damaging	Het
Pcdhb18	G	A	18: 37,623,537 (GRCm39)	R289Q	probably benign	Het
Pcyox1l	C	T	18: 61,832,359 (GRCm39)		probably null	Het
Plxnb2	T	C	15: 89,044,962 (GRCm39)	T1128A	possibly damaging	Het
Prex1	T	C	2: 166,425,127 (GRCm39)	T960A	probably benign	Het
Prkaa2	A	C	4: 104,893,291 (GRCm39)	*553G	probably null	Het
Rasgrp4	A	G	7: 28,844,639 (GRCm39)	D297G	probably damaging	Het
Serpinb3d	T	C	1: 107,007,027 (GRCm39)	K227R	probably benign	Het
Sgsm1	A	T	5: 113,398,822 (GRCm39)	I750N	probably damaging	Het
Shtn1	T	A	19: 59,020,673 (GRCm39)	K183M	probably damaging	Het
Skic3	A	G	13: 76,303,852 (GRCm39)	T1257A	probably benign	Het
Slc22a30	T	C	19: 8,381,945 (GRCm39)	T109A	probably benign	Het
Slco1c1	A	G	6: 141,487,929 (GRCm39)	D99G	probably damaging	Het
Tcf25	T	A	8: 124,122,354 (GRCm39)		probably null	Het
Tex10	A	G	4: 48,452,928 (GRCm39)	V677A	probably benign	Het
Tmem131l	A	G	3: 83,847,879 (GRCm39)	S329P	probably benign	Het
Trappc10	T	A	10: 78,058,573 (GRCm39)	N136I	probably damaging	Het
Trpt1	T	C	19: 6,975,906 (GRCm39)	F173L	probably benign	Het
Ube4b	G	A	4: 149,421,925 (GRCm39)	R955C	probably damaging	Het
Usp34	C	A	11: 23,371,340 (GRCm39)	P1840T	probably benign	Het
Vmn1r27	A	T	6: 58,192,985 (GRCm39)	N6K	possibly damaging	Het
Wdr25	T	C	12: 108,993,347 (GRCm39)	V521A	possibly damaging	Het
Wdr64	G	A	1: 175,639,623 (GRCm39)	E1031K	possibly damaging	Het
Wnt10a	A	G	1: 74,839,755 (GRCm39)	N147S	probably damaging	Het
Zbed5	T	C	5: 129,931,059 (GRCm39)	I336T	possibly damaging	Het
Zfp758	T	A	17: 22,594,796 (GRCm39)	H427Q	probably damaging	Het
Zfp961	C	A	8: 72,722,070 (GRCm39)	H194Q	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
R4868:Sdf4	UTSW	4	156,093,642 (GRCm39)	missense	probably damaging	1.00
R5752:Sdf4	UTSW	4	156,080,761 (GRCm39)	missense	probably damaging	1.00
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'- TGACTTAACTGCTCACCCAC -3'
(R):5'- GTTAAGGCTGCAGTCTCCTG -3'

Sequencing Primer
(F):5'- ACAATTTTCCTTACAGACCCTGG -3'
(R):5'- TGACTTCACCCACTTCACCCAG -3'

Posted On

2017-12-01