Mutagenetix > Incidental Mutations

Incidental Mutation 'R1489:Atg9a'

163574

Institutional Source

Beutler Lab

Gene Symbol

Atg9a

Ensembl Gene

ENSMUSG00000033124

Gene Name

autophagy related 9A

Synonyms

Apg9l1

MMRRC Submission

039541-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1489 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75180860-75192196 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 75186090 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 427 (D427V)

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: D427V

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

SMART Domains

Protein: ENSMUSP00000047449
Gene: ENSMUSG00000033124
AA Change: D427V

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

probably benign
Transcript: ENSMUST00000187785

Predicted Effect

probably damaging
Transcript: ENSMUST00000188347
AA Change: D427V

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

SMART Domains

Protein: ENSMUSP00000139731
Gene: ENSMUSG00000033124
AA Change: D427V

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: D427V

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

SMART Domains

Protein: ENSMUSP00000139641
Gene: ENSMUSG00000033124
AA Change: D427V

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: D419V

Meta Mutation Damage Score

0.9677

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.7%
20x: 93.9%

Validation Efficiency

96% (52/54)

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: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700097O09Rik	A	G	12: 55,059,510	S143P	possibly damaging	Het
4930522H14Rik	T	C	4: 109,505,457	K218E	possibly damaging	Het
Abcb1a	T	A	5: 8,686,300		probably null	Het
Adam39	A	G	8: 40,824,994	T141A	possibly damaging	Het
Adam6b	T	A	12: 113,491,451	S629R	probably benign	Het
Ap3b2	C	A	7: 81,463,690	E924*	probably null	Het
Armc3	A	T	2: 19,310,047	Y856F	probably benign	Het
Asap1	A	G	15: 64,172,730	L142P	probably damaging	Het
Atl2	G	A	17: 79,852,706	A17V	probably benign	Het
Atxn2l	A	T	7: 126,496,467	S379T	probably damaging	Het
C1ql3	G	T	2: 13,010,642	P69Q	possibly damaging	Het
Cap2	A	T	13: 46,609,635	I114F	probably damaging	Het
Cox16	T	C	12: 81,474,615	N135S	probably null	Het
Dnajc13	A	T	9: 104,231,035	H180Q	possibly damaging	Het
Dpy19l3	A	T	7: 35,725,410	Y73*	probably null	Het
Duox2	T	A	2: 122,293,396	M436L	probably benign	Het
Exoc6	T	A	19: 37,597,120	M481K	possibly damaging	Het
Fbxw2	GCCCCC	GCCCCCCCC	2: 34,812,817		probably benign	Het
Fmn1	T	A	2: 113,365,212	V419E	unknown	Het
Fndc4	T	C	5: 31,293,451	*232W	probably null	Het
Foxc1	C	T	13: 31,808,612	R469*	probably null	Het
Fsip2	A	G	2: 82,979,811	H2158R	probably benign	Het
Ghdc	C	T	11: 100,768,257	G373D	probably benign	Het
Gm10330	A	T	12: 23,780,031	S50T	probably benign	Het
Gm8251	A	G	1: 44,057,790	F1383L	probably benign	Het
Gm8251	T	C	1: 44,061,507	I144V	probably benign	Het
Hlx	G	T	1: 184,731,987	A52D	probably damaging	Het
Lonrf1	A	G	8: 36,222,954	V650A	probably damaging	Het
Map1a	T	C	2: 121,300,437	V578A	possibly damaging	Het
Mbd3	C	G	10: 80,393,906	D190H	probably damaging	Het
Mcpt9	T	C	14: 56,027,519	K175R	probably benign	Het
Mia3	A	G	1: 183,338,674	S85P	probably benign	Het
Myrip	T	C	9: 120,432,529	F403L	probably damaging	Het
Nox4	A	G	7: 87,304,889	Y134C	probably damaging	Het
Numb	A	G	12: 83,795,443	L642P	probably damaging	Het
Pappa	A	T	4: 65,180,948	Y568F	possibly damaging	Het
Pdzrn4	T	C	15: 92,677,712	L333P	probably benign	Het
Prl	A	T	13: 27,057,636	S3C	probably damaging	Het
Ptprc	T	C	1: 138,120,086	T60A	possibly damaging	Het
Rbm10	C	T	X: 20,637,664		probably benign	Het
Slc7a7	C	T	14: 54,408,646	R120H	probably damaging	Het
Smpd1	T	C	7: 105,556,554		probably null	Het
Spta1	A	G	1: 174,231,325	E1942G	probably damaging	Het
Tmem38a	A	G	8: 72,579,635	Y66C	probably damaging	Het
Tnnt1	A	T	7: 4,507,525	Y232*	probably null	Het
Tpte	T	C	8: 22,349,389		probably null	Het
Virma	T	C	4: 11,521,164	V907A	probably damaging	Het
Vmn1r174	C	T	7: 23,754,556	Q216*	probably null	Het
Zswim3	T	C	2: 164,819,981	V127A	probably benign	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
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
R2172:Atg9a	UTSW	1	75185685	missense	probably damaging	0.99
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
R9441:Atg9a	UTSW	1	75186442	missense	possibly damaging	0.92
R9442:Atg9a	UTSW	1	75186442	missense	possibly damaging	0.92
R9448:Atg9a	UTSW	1	75186205	missense	probably benign	0.35
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'- CCACTCACTGCCTTGTACTGGAAG -3'
(R):5'- TCAATGAGCTGGAGCATGAGCTG -3'

Sequencing Primer
(F):5'- AGAGCTGGGCAAACTCGTC -3'
(R):5'- CAAGAATGGTGCCTTCTTCG -3'

Posted On

2014-03-28