Mutagenetix > Incidental Mutation

Incidental Mutation 'R5369:Snx9'

429577

Institutional Source

Beutler Lab

Gene Symbol

Snx9

Ensembl Gene

ENSMUSG00000002365

Gene Name

sorting nexin 9

Synonyms

SH3PX1, SDP1

MMRRC Submission

042946-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.861) question?

Stock #

R5369 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

5841329-5931954 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 5920580 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 399 (C399S)

Ref Sequence

ENSEMBL: ENSMUSP00000002436 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002436]

AlphaFold

Q91VH2

PDB Structure

Solution structure of the SH3 domain from mouse sorting nexin-9 [SOLUTION NMR]

Predicted Effect

probably damaging
Transcript: ENSMUST00000002436
AA Change: C399S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000002436
Gene: ENSMUSG00000002365
AA Change: C399S

Domain	Start	End	E-Value	Type
SH3	3	61	1.51e-16	SMART
low complexity region	84	100	N/A	INTRINSIC
low complexity region	160	170	N/A	INTRINSIC
PX	247	357	4.15e-23	SMART
Pfam:BAR_3_WASP_bdg	358	593	2.4e-120	PFAM

Meta Mutation Damage Score

0.5515

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.6%

Validation Efficiency

99% (77/78)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the sorting nexin family. Members of this family contain a phosphoinositide binding domain, and are involved in intracellular trafficking. The encoded protein does not contain a coiled coil region, like some family members, but does contain a SRC homology domain near its N-terminus. The encoded protein is reported to have a variety of interaction partners, including of adaptor protein 2 , dynamin, tyrosine kinase non-receptor 2, Wiskott-Aldrich syndrome-like, and ARP3 actin-related protein 3. The encoded protein is implicated in several stages of intracellular trafficking, including endocytosis, macropinocytosis, and F-actin nucleation. [provided by RefSeq, Jul 2013]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210010C04Rik	T	A	6: 41,033,006 (GRCm38)	R131S	probably benign	Het
A2ml1	T	C	6: 128,568,833 (GRCm38)	T444A	probably damaging	Het
A330070K13Rik	G	A	5: 130,379,091 (GRCm38)		probably benign	Het
Abcb8	C	T	5: 24,400,139 (GRCm38)	R108C	possibly damaging	Het
Acbd5	T	A	2: 23,112,510 (GRCm38)	L508Q	probably damaging	Het
Asb15	T	C	6: 24,562,564 (GRCm38)	V175A	probably benign	Het
B3galnt2	T	C	13: 13,994,425 (GRCm38)		probably null	Het
BC024139	A	C	15: 76,120,222 (GRCm38)	S711R	probably benign	Het
Bod1l	A	G	5: 41,827,183 (GRCm38)	I508T	probably damaging	Het
Btnl6	T	A	17: 34,507,985 (GRCm38)	R524*	probably null	Het
C3	C	A	17: 57,221,159 (GRCm38)	D687Y	probably benign	Het
Ccbe1	G	A	18: 66,061,414 (GRCm38)	A367V	probably benign	Het
Ccr1	A	T	9: 123,964,289 (GRCm38)	M68K	probably damaging	Het
Cd27	T	A	6: 125,234,364 (GRCm38)		probably benign	Het
Celf2	C	A	2: 7,081,081 (GRCm38)		probably benign	Het
Cfap54	T	C	10: 93,061,257 (GRCm38)		probably benign	Het
Cfap97	A	G	8: 46,169,650 (GRCm38)	K26E	probably damaging	Het
Clcn4	T	A	7: 7,296,033 (GRCm38)	I48F	probably benign	Het
Cnot7	A	T	8: 40,494,020 (GRCm38)	N238K	probably benign	Het
Colec12	A	G	18: 9,866,750 (GRCm38)	I654V	unknown	Het
Dip2a	A	G	10: 76,292,360 (GRCm38)	I22T	probably damaging	Het
Eif4g3	C	T	4: 138,183,334 (GRCm38)	T1375M	possibly damaging	Het
Eml5	C	T	12: 98,858,783 (GRCm38)	G725D	probably damaging	Het
F12	T	C	13: 55,418,491 (GRCm38)	E496G	probably benign	Het
Fam227a	A	T	15: 79,615,436 (GRCm38)	S573T	probably benign	Het
Fnip1	T	C	11: 54,502,589 (GRCm38)	V593A	probably benign	Het
Focad	T	A	4: 88,121,373 (GRCm38)		probably benign	Het
Frem1	A	G	4: 83,001,739 (GRCm38)	I460T	possibly damaging	Het
Galnt10	T	G	11: 57,765,747 (GRCm38)		probably null	Het
Gm5592	A	T	7: 41,218,211 (GRCm38)		probably benign	Het
Gm6185	A	T	1: 161,209,760 (GRCm38)		noncoding transcript	Het
Gm7935	A	T	15: 74,081,114 (GRCm38)		noncoding transcript	Het
Grb14	C	T	2: 64,917,309 (GRCm38)	V369I	probably benign	Het
Gstm5	G	A	3: 107,898,466 (GRCm38)	A198T	probably damaging	Het
Herc2	T	A	7: 56,182,700 (GRCm38)	V3048D	probably damaging	Het
Htra4	T	G	8: 25,033,569 (GRCm38)	I327L	possibly damaging	Het
Ifi209	T	C	1: 173,637,307 (GRCm38)	M1T	probably null	Het
Ints6	T	C	14: 62,743,935 (GRCm38)	T135A	probably damaging	Het
Itpr1	T	A	6: 108,519,424 (GRCm38)	I2604N	probably damaging	Het
Krt6a	T	A	15: 101,692,558 (GRCm38)	M268L	probably benign	Het
Lrp1b	G	T	2: 41,004,613 (GRCm38)	S2201*	probably null	Het
Lrp2	T	C	2: 69,459,560 (GRCm38)	N3645S	probably benign	Het
Lrrc15	A	T	16: 30,272,904 (GRCm38)	I539N	possibly damaging	Het
Map3k6	T	C	4: 133,247,681 (GRCm38)	I675T	probably damaging	Het
Map3k9	T	A	12: 81,722,052 (GRCm38)	E1074V	probably damaging	Het
Med13l	T	A	5: 118,724,010 (GRCm38)	S339R	probably benign	Het
Mrps18a	T	C	17: 46,125,626 (GRCm38)		probably benign	Het
Nat8f2	G	T	6: 85,867,872 (GRCm38)	Y169*	probably null	Het
Nlrp1b	A	G	11: 71,181,799 (GRCm38)	I406T	probably benign	Het
Npc1l1	A	G	11: 6,217,705 (GRCm38)		probably null	Het
Olfr202	A	T	16: 59,284,380 (GRCm38)	M39K	probably damaging	Het
Olfr419	A	G	1: 174,250,441 (GRCm38)	V162A	probably damaging	Het
Ostf1	C	T	19: 18,581,325 (GRCm38)	G198E	probably benign	Het
Pcsk5	A	G	19: 17,581,255 (GRCm38)	V596A	probably damaging	Het
Pde4c	T	C	8: 70,750,105 (GRCm38)	*647Q	probably null	Het
Pkm	A	T	9: 59,670,634 (GRCm38)	I245F	probably damaging	Het
Ptprj	T	C	2: 90,469,641 (GRCm38)	H179R	probably benign	Het
Rapgef2	A	T	3: 79,069,432 (GRCm38)	S1356T	probably benign	Het
Rbm45	T	A	2: 76,370,250 (GRCm38)	L41Q	probably damaging	Het
Rsf1	ATGGCG	ATGGCGACGGTGGCG	7: 97,579,904 (GRCm38)		probably benign	Het
Scara5	CG	C	14: 65,759,662 (GRCm38)		probably null	Het
Scel	A	T	14: 103,586,493 (GRCm38)	I386F	probably benign	Het
Serpinb5	A	T	1: 106,881,757 (GRCm38)	N298Y	possibly damaging	Het
Sirt3	A	T	7: 140,869,493 (GRCm38)	L180Q	probably damaging	Het
Slc24a2	C	T	4: 86,991,388 (GRCm38)	V698I	probably damaging	Het
Slc43a3	A	T	2: 84,957,723 (GRCm38)	H483L	probably damaging	Het
Snrnp35	A	G	5: 124,490,199 (GRCm38)	D25G	probably benign	Het
Snrnp40	T	C	4: 130,362,646 (GRCm38)	S55P	probably damaging	Het
Soga1	T	C	2: 157,040,734 (GRCm38)	E466G	probably damaging	Het
Ttbk2	T	C	2: 120,825,262 (GRCm38)		probably benign	Het
Vmn1r1	A	G	1: 182,157,776 (GRCm38)	V108A	possibly damaging	Het
Vmn1r201	T	A	13: 22,475,502 (GRCm38)	N295K	probably benign	Het
Zfp292	G	A	4: 34,807,491 (GRCm38)	P1851L	possibly damaging	Het
Zfp472	A	T	17: 32,977,743 (GRCm38)	D264V	probably damaging	Het

Other mutations in Snx9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00332:Snx9	APN	17	5,899,361 (GRCm38)	missense	probably benign
IGL00417:Snx9	APN	17	5,891,897 (GRCm38)	missense	probably benign	0.03
IGL01827:Snx9	APN	17	5,887,012 (GRCm38)	missense	probably benign	0.04
IGL02531:Snx9	APN	17	5,891,820 (GRCm38)	missense	probably benign
IGL02710:Snx9	APN	17	5,908,598 (GRCm38)	missense	probably damaging	1.00
IGL03088:Snx9	APN	17	5,924,610 (GRCm38)	missense	probably benign
san_angelo	UTSW	17	5,891,809 (GRCm38)	nonsense	probably null
PIT4495001:Snx9	UTSW	17	5,920,126 (GRCm38)	missense	possibly damaging	0.54
R0555:Snx9	UTSW	17	5,918,413 (GRCm38)	missense	probably damaging	0.97
R1015:Snx9	UTSW	17	5,920,127 (GRCm38)	missense	probably benign	0.12
R1065:Snx9	UTSW	17	5,902,361 (GRCm38)	splice site	probably benign
R1421:Snx9	UTSW	17	5,902,484 (GRCm38)	missense	probably benign	0.45
R1657:Snx9	UTSW	17	5,918,436 (GRCm38)	missense	possibly damaging	0.65
R1823:Snx9	UTSW	17	5,920,671 (GRCm38)	missense	probably damaging	1.00
R1914:Snx9	UTSW	17	5,928,256 (GRCm38)	missense	possibly damaging	0.65
R3703:Snx9	UTSW	17	5,928,200 (GRCm38)	splice site	probably null
R3871:Snx9	UTSW	17	5,891,781 (GRCm38)	missense	probably benign	0.00
R4375:Snx9	UTSW	17	5,908,626 (GRCm38)	nonsense	probably null
R4412:Snx9	UTSW	17	5,908,394 (GRCm38)	missense	probably damaging	0.96
R4669:Snx9	UTSW	17	5,927,224 (GRCm38)	missense	probably damaging	1.00
R4974:Snx9	UTSW	17	5,902,519 (GRCm38)	splice site	probably null
R5038:Snx9	UTSW	17	5,887,073 (GRCm38)	missense	probably benign	0.12
R5137:Snx9	UTSW	17	5,928,253 (GRCm38)	missense	probably damaging	1.00
R5459:Snx9	UTSW	17	5,920,638 (GRCm38)	missense	probably damaging	0.99
R5624:Snx9	UTSW	17	5,891,809 (GRCm38)	nonsense	probably null
R5847:Snx9	UTSW	17	5,924,621 (GRCm38)	missense	possibly damaging	0.94
R5953:Snx9	UTSW	17	5,908,403 (GRCm38)	missense	probably damaging	1.00
R5953:Snx9	UTSW	17	5,908,402 (GRCm38)	missense	probably damaging	1.00
R6263:Snx9	UTSW	17	5,887,049 (GRCm38)	missense	probably damaging	0.98
R6481:Snx9	UTSW	17	5,922,209 (GRCm38)	critical splice donor site	probably null
R6491:Snx9	UTSW	17	5,920,162 (GRCm38)	missense	probably benign	0.00
R7873:Snx9	UTSW	17	5,918,476 (GRCm38)	missense	possibly damaging	0.81
R8471:Snx9	UTSW	17	5,890,090 (GRCm38)	missense	probably damaging	1.00
R9451:Snx9	UTSW	17	5,899,493 (GRCm38)	missense	probably damaging	0.99
R9748:Snx9	UTSW	17	5,899,395 (GRCm38)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CAAGGTCTGTCCCATTGTAGGC -3'
(R):5'- ATGACGTTTCCTGAGCTACCTC -3'

Sequencing Primer
(F):5'- CCCATTGTAGGCATCATGCTGG -3'
(R):5'- ACGTTTCCTGAGCTACCTCTGTTATC -3'

Posted On

2016-09-06