Mutagenetix > Incidental Mutations

Incidental Mutation 'R2172:Atg9a'

237518

Institutional Source

Beutler Lab

Gene Symbol

Atg9a

Ensembl Gene

ENSMUSG00000033124

Gene Name

autophagy related 9A

Synonyms

Apg9l1

MMRRC Submission

040174-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R2172 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

75180860-75192196 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 75185685 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 527 (R527L)

Ref Sequence

ENSEMBL: ENSMUSP00000139641 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040689] [ENSMUST00000186744] [ENSMUST00000188347] [ENSMUST00000189665] [ENSMUST00000189702]

AlphaFold

Q68FE2

Predicted Effect

probably damaging
Transcript: ENSMUST00000040689
AA Change: R527L

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000047449
Gene: ENSMUSG00000033124
AA Change: R527L

Domain	Start	End	E-Value	Type
transmembrane domain	70	92	N/A	INTRINSIC
transmembrane domain	126	148	N/A	INTRINSIC
Pfam:APG9	173	530	3.4e-134	PFAM
low complexity region	588	599	N/A	INTRINSIC
low complexity region	607	621	N/A	INTRINSIC
Blast:HELICc	692	733	1e-13	BLAST
low complexity region	734	755	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000185727

Predicted Effect

probably benign
Transcript: ENSMUST00000186744

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000187601

Predicted Effect

unknown
Transcript: ENSMUST00000187785
AA Change: R86L

Predicted Effect

probably damaging
Transcript: ENSMUST00000188347
AA Change: R527L

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139731
Gene: ENSMUSG00000033124
AA Change: R527L

Domain	Start	End	E-Value	Type
transmembrane domain	70	92	N/A	INTRINSIC
transmembrane domain	126	148	N/A	INTRINSIC
Pfam:APG9	172	533	2.4e-140	PFAM
low complexity region	588	599	N/A	INTRINSIC
low complexity region	607	621	N/A	INTRINSIC
Blast:HELICc	692	733	1e-13	BLAST
low complexity region	734	755	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000188430

Predicted Effect

probably benign
Transcript: ENSMUST00000189665

SMART Domains

Protein: ENSMUSP00000140012
Gene: ENSMUSG00000033124

Domain	Start	End	E-Value	Type
transmembrane domain	70	92	N/A	INTRINSIC
transmembrane domain	126	148	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000189702
AA Change: R527L

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139641
Gene: ENSMUSG00000033124
AA Change: R527L

Domain	Start	End	E-Value	Type
transmembrane domain	70	92	N/A	INTRINSIC
transmembrane domain	126	148	N/A	INTRINSIC
Pfam:APG9	172	533	2.4e-140	PFAM
low complexity region	588	599	N/A	INTRINSIC
low complexity region	607	621	N/A	INTRINSIC
Blast:HELICc	692	733	1e-13	BLAST
low complexity region	734	755	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000189820
AA Change: R519L

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.4%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a null mutation all die within 1 day of birth and display impaired autophagy. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arap3	T	A	18: 37,990,560	E441V	probably damaging	Het
Arfip2	T	A	7: 105,637,988	D64V	probably damaging	Het
Atp1a1	T	G	3: 101,590,548	I308L	probably benign	Het
Bcan	T	A	3: 87,996,581	Y199F	probably damaging	Het
Bsn	T	C	9: 108,109,992		probably benign	Het
Ccdc158	A	T	5: 92,632,508	L902H	probably damaging	Het
Dnah7b	A	G	1: 46,124,512	Y492C	probably benign	Het
Dnah9	G	T	11: 66,072,779	H1783N	probably damaging	Het
Dpep2	A	G	8: 105,988,998	V320A	possibly damaging	Het
Dsc2	A	G	18: 20,045,502	Y282H	probably damaging	Het
Egfr	C	T	11: 16,911,562	P1114S	probably benign	Het
Fastkd1	A	G	2: 69,700,133	S560P	probably damaging	Het
Gm10696	T	G	3: 94,176,298	K69Q	possibly damaging	Het
Gm14295	G	A	2: 176,811,102	R795Q	possibly damaging	Het
Gpr155	C	T	2: 73,382,127	V51I	probably benign	Het
Gsap	G	A	5: 21,222,440		probably null	Het
Hecw1	T	A	13: 14,377,706	I103F	probably damaging	Het
Herc3	T	A	6: 58,887,437	N685K	probably damaging	Het
Hnrnph1	T	A	11: 50,382,816	D244E	probably benign	Het
Hydin	A	G	8: 110,582,049	E3989G	probably benign	Het
Ibsp	T	C	5: 104,310,430	Y278H	probably damaging	Het
Ift57	T	G	16: 49,759,340	N291K	probably benign	Het
Il15ra	A	G	2: 11,723,571	T149A	possibly damaging	Het
Ints5	C	T	19: 8,896,282	T535I	possibly damaging	Het
Jarid2	T	C	13: 44,902,539	L268P	probably damaging	Het
Klhdc7a	T	A	4: 139,965,810	T609S	probably benign	Het
Lrrc49	A	G	9: 60,602,682	V429A	probably benign	Het
Lsm3	T	C	6: 91,522,272	V87A	possibly damaging	Het
Man1c1	G	C	4: 134,703,438	P11R	probably damaging	Het
Map1a	G	T	2: 121,307,932	V2726L	probably damaging	Het
Marveld3	A	C	8: 109,961,846	S88A	probably benign	Het
Mcm9	T	C	10: 53,548,574	D640G	probably damaging	Het
Mettl4	A	G	17: 94,733,163	I399T	probably benign	Het
Mmp27	T	A	9: 7,577,378	L274*	probably null	Het
Nacc2	A	C	2: 26,060,223	D500E	probably benign	Het
Nprl3	T	A	11: 32,234,894	M372L	probably benign	Het
Olfr478	A	T	7: 108,031,467	I292N	probably damaging	Het
Otud7b	T	G	3: 96,153,520		probably null	Het
Pcx	G	A	19: 4,620,881	R1070H	probably benign	Het
Ptprq	C	T	10: 107,590,994	W1560*	probably null	Het
Puf60	A	T	15: 76,070,464	I520N	probably damaging	Het
Qars	C	T	9: 108,509,200	R143C	probably damaging	Het
Rfx3	G	A	19: 27,815,494	Q322*	probably null	Het
Samd14	G	T	11: 95,014,391	V10L	probably benign	Het
Setd2	G	A	9: 110,549,844	R909Q	probably benign	Het
Sh2d4a	T	C	8: 68,296,664	S117P	probably benign	Het
Sharpin	C	A	15: 76,350,666		probably benign	Het
Skor1	C	A	9: 63,145,122	A494S	possibly damaging	Het
Slc41a2	T	C	10: 83,283,774	T375A	probably benign	Het
Sparc	G	A	11: 55,395,801	Q324*	probably null	Het
Srebf1	T	C	11: 60,206,502	T171A	probably benign	Het
Srrd	A	G	5: 112,341,122	I54T	possibly damaging	Het
Tecpr1	G	T	5: 144,196,417	Q1072K	probably damaging	Het
Tecpr1	A	T	5: 144,211,456	V377E	probably benign	Het
Tln1	T	A	4: 43,545,721	H919L	probably benign	Het
Tm9sf3	C	T	19: 41,217,420	S516N	probably damaging	Het
Trpa1	T	A	1: 14,881,656	T940S	probably benign	Het
Trpv4	G	A	5: 114,644,710	R64C	probably damaging	Het
Tufm	A	G	7: 126,488,847	E174G	probably benign	Het
Urb2	A	G	8: 124,031,102	T1183A	probably damaging	Het
Virma	A	T	4: 11,527,843	M1245L	possibly damaging	Het
Vmn2r32	T	C	7: 7,474,615	Y259C	probably damaging	Het
Zfp329	A	G	7: 12,810,767	F277L	probably damaging	Het
Zfp683	C	T	4: 134,055,795	T190I	possibly damaging	Het

Other mutations in Atg9a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01464:Atg9a	APN	1	75190366	missense	probably damaging	1.00
IGL02041:Atg9a	APN	1	75183104	missense	possibly damaging	0.47
IGL03367:Atg9a	APN	1	75187957	missense	probably benign	0.18
PIT4494001:Atg9a	UTSW	1	75187953	nonsense	probably null
R0054:Atg9a	UTSW	1	75184499	missense	probably damaging	1.00
R0054:Atg9a	UTSW	1	75184499	missense	probably damaging	1.00
R0408:Atg9a	UTSW	1	75185295	missense	probably damaging	1.00
R0520:Atg9a	UTSW	1	75186534	nonsense	probably null
R0653:Atg9a	UTSW	1	75190328	missense	probably damaging	0.96
R0666:Atg9a	UTSW	1	75185090	missense	probably damaging	0.99
R0961:Atg9a	UTSW	1	75186746	missense	probably damaging	0.99
R1489:Atg9a	UTSW	1	75186090	missense	probably damaging	1.00
R1490:Atg9a	UTSW	1	75185745	missense	possibly damaging	0.70
R1692:Atg9a	UTSW	1	75190355	missense	probably benign	0.04
R1997:Atg9a	UTSW	1	75189626	missense	probably benign	0.33
R2005:Atg9a	UTSW	1	75185991	missense	probably benign	0.18
R4004:Atg9a	UTSW	1	75186451	missense	probably damaging	1.00
R4105:Atg9a	UTSW	1	75185959	missense	probably damaging	1.00
R5010:Atg9a	UTSW	1	75186060	splice site	probably null
R5220:Atg9a	UTSW	1	75185728	missense	probably damaging	1.00
R5898:Atg9a	UTSW	1	75186272	missense	probably damaging	1.00
R6295:Atg9a	UTSW	1	75185058	missense	probably benign	0.01
R6390:Atg9a	UTSW	1	75187981	missense	probably damaging	1.00
R7312:Atg9a	UTSW	1	75188092	missense	probably damaging	1.00
R7729:Atg9a	UTSW	1	75184560	missense	probably benign	0.34
R8111:Atg9a	UTSW	1	75187722	missense	probably damaging	1.00
R8210:Atg9a	UTSW	1	75185283	missense	probably damaging	1.00
R8210:Atg9a	UTSW	1	75186365	missense	probably damaging	1.00
R8256:Atg9a	UTSW	1	75186919	missense	possibly damaging	0.88
R8319:Atg9a	UTSW	1	75185698	nonsense	probably null
R8321:Atg9a	UTSW	1	75185698	nonsense	probably null
R8382:Atg9a	UTSW	1	75185698	nonsense	probably null
R8406:Atg9a	UTSW	1	75190384	missense	probably damaging	1.00
R8482:Atg9a	UTSW	1	75186226	missense	probably damaging	0.99
R8855:Atg9a	UTSW	1	75185223	missense	probably damaging	1.00
R8866:Atg9a	UTSW	1	75185223	missense	probably damaging	1.00
R9381:Atg9a	UTSW	1	75186082	missense	probably benign
RF021:Atg9a	UTSW	1	75182629	missense	probably damaging	0.96
Z1176:Atg9a	UTSW	1	75186559	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACTGGGTCAGTCACTTGAACTG -3'
(R):5'- CTGCTAGAGACTGGCTGGTATC -3'

Sequencing Primer
(F):5'- GAATCCAGTCAGATTCCTGGTGAC -3'
(R):5'- GTCCTGCTTGCGGGTAAC -3'

Posted On

2014-10-02