Mutagenetix > Incidental Mutation

Incidental Mutation 'R0666:Atg9a'

61999

Institutional Source

Beutler Lab

Gene Symbol

Atg9a

Ensembl Gene

ENSMUSG00000033124

Gene Name

autophagy related 9A

Synonyms

Apg9l1

MMRRC Submission

038851-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0666 (G1)

Quality Score

121

Status

Validated

Chromosome

Chromosomal Location

75157509-75168654 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 75161734 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 604 (L604P)

Ref Sequence

ENSEMBL: ENSMUSP00000139641 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027396] [ENSMUST00000040689] [ENSMUST00000189702] [ENSMUST00000188347] [ENSMUST00000189665]

AlphaFold

Q68FE2

Predicted Effect

probably benign
Transcript: ENSMUST00000027396

SMART Domains

Protein: ENSMUSP00000027396
Gene: ENSMUSG00000026198

Domain	Start	End	E-Value	Type
Pfam:MTABC_N	6	255	7.8e-80	PFAM
Pfam:ABC_membrane	265	544	3.7e-34	PFAM
AAA	615	816	1.29e-19	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000040689
AA Change: L604P

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000047449
Gene: ENSMUSG00000033124
AA Change: L604P

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: ENSMUST00000159219

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160081

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161103

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000185727

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000187601

Predicted Effect

probably damaging
Transcript: ENSMUST00000189702
AA Change: L604P

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139641
Gene: ENSMUSG00000033124
AA Change: L604P

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

probably damaging
Transcript: ENSMUST00000188347
AA Change: L604P

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139731
Gene: ENSMUSG00000033124
AA Change: L604P

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: ENSMUST00000187785
AA Change: L163P

Predicted Effect

unknown
Transcript: ENSMUST00000189820
AA Change: L596P

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

Meta Mutation Damage Score

0.3098

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.7%
20x: 95.7%

Validation Efficiency

100% (89/89)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akap6	T	A	12: 52,958,591 (GRCm39)	V782E	probably damaging	Het
Atp1a3	T	C	7: 24,689,974 (GRCm39)	I482V	probably benign	Het
Bltp2	T	G	11: 78,178,813 (GRCm39)	M2026R	probably damaging	Het
Bltp2	T	A	11: 78,168,038 (GRCm39)	L1491*	probably null	Het
Ccdc18	T	G	5: 108,311,530 (GRCm39)	V412G	probably benign	Het
Ccn6	T	C	10: 39,027,285 (GRCm39)	R316G	probably benign	Het
Cct6a	A	G	5: 129,871,449 (GRCm39)		noncoding transcript	Het
Clpx	A	G	9: 65,217,507 (GRCm39)	N25S	probably damaging	Het
Cnpy2	T	A	10: 128,162,894 (GRCm39)	C171*	probably null	Het
Cntnap3	C	T	13: 64,905,211 (GRCm39)	D857N	probably damaging	Het
Col5a1	A	G	2: 27,922,697 (GRCm39)	Y255C	probably damaging	Het
Coro7	A	T	16: 4,449,775 (GRCm39)	F638Y	possibly damaging	Het
Cpd	A	G	11: 76,673,153 (GRCm39)	F1331L	probably damaging	Het
Csmd1	A	T	8: 16,119,063 (GRCm39)	I1842N	possibly damaging	Het
Dgkg	T	A	16: 22,381,480 (GRCm39)	D490V	probably damaging	Het
Dnah9	A	T	11: 65,976,284 (GRCm39)	M1255K	probably benign	Het
E2f1	A	G	2: 154,402,849 (GRCm39)	V306A	probably benign	Het
Entpd1	A	G	19: 40,648,350 (GRCm39)		probably benign	Het
Esrrb	T	A	12: 86,552,676 (GRCm39)	I222N	probably benign	Het
Flt4	G	T	11: 49,516,274 (GRCm39)	A126S	possibly damaging	Het
Galnt11	C	T	5: 25,457,145 (GRCm39)	T237I	possibly damaging	Het
Galnt2l	A	T	8: 122,997,727 (GRCm39)		probably benign	Het
Gbf1	A	G	19: 46,250,983 (GRCm39)		probably benign	Het
H2-T9	T	C	17: 36,438,726 (GRCm39)	T222A	possibly damaging	Het
Herc1	T	A	9: 66,392,170 (GRCm39)		probably benign	Het
Hsph1	T	C	5: 149,554,967 (GRCm39)	Y105C	probably damaging	Het
Il23r	T	C	6: 67,411,664 (GRCm39)	T358A	probably benign	Het
Il2ra	C	T	2: 11,647,884 (GRCm39)		probably benign	Het
Kbtbd4	G	T	2: 90,744,459 (GRCm39)		probably benign	Het
Kcnt1	A	G	2: 25,781,255 (GRCm39)		probably benign	Het
Kng2	A	G	16: 22,815,872 (GRCm39)		probably benign	Het
Lap3	C	T	5: 45,669,270 (GRCm39)	T473I	possibly damaging	Het
Lrrk2	T	C	15: 91,641,273 (GRCm39)		probably null	Het
Map1s	A	G	8: 71,366,696 (GRCm39)	N534D	possibly damaging	Het
Mtg1	G	A	7: 139,724,257 (GRCm39)	V122I	probably benign	Het
Myadm	T	A	7: 3,345,865 (GRCm39)	I209K	probably damaging	Het
Ntsr2	G	A	12: 16,703,981 (GRCm39)	V75I	probably benign	Het
Or4b1b	A	T	2: 90,112,212 (GRCm39)	S236T	probably damaging	Het
Or8u10	G	A	2: 85,915,557 (GRCm39)	A188V	probably benign	Het
Pfn1	T	C	11: 70,545,192 (GRCm39)	T39A	probably benign	Het
Pipox	T	A	11: 77,774,651 (GRCm39)	K144M	probably benign	Het
Plekhh1	G	A	12: 79,115,889 (GRCm39)	E811K	probably damaging	Het
Pnpla3	T	A	15: 84,063,506 (GRCm39)	W295R	probably benign	Het
Prkacb	T	A	3: 146,457,273 (GRCm39)	T136S	probably damaging	Het
Ralbp1	T	A	17: 66,161,124 (GRCm39)	N473I	probably benign	Het
Rbp4	G	A	19: 38,106,908 (GRCm39)	T127M	probably damaging	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rps3a1	G	A	3: 86,045,424 (GRCm39)		probably benign	Het
Scg3	G	T	9: 75,551,222 (GRCm39)	Y429*	probably null	Het
Shisal2b	G	T	13: 104,994,862 (GRCm39)	T95K	possibly damaging	Het
Spag5	T	C	11: 78,204,222 (GRCm39)	S492P	probably damaging	Het
St7	T	A	6: 17,934,238 (GRCm39)	M540K	probably damaging	Het
Stxbp3	C	A	3: 108,712,618 (GRCm39)	V281F	possibly damaging	Het
Sun5	A	G	2: 153,700,968 (GRCm39)	V242A	possibly damaging	Het
Susd5	G	T	9: 113,924,852 (GRCm39)	R245L	possibly damaging	Het
Syne2	A	G	12: 75,969,787 (GRCm39)	E954G	probably damaging	Het
Synpo2	A	T	3: 122,907,708 (GRCm39)	V536E	probably damaging	Het
Tas2r140	T	C	6: 133,032,405 (GRCm39)	I118V	probably benign	Het
Tbx18	C	A	9: 87,606,462 (GRCm39)	V228L	probably benign	Het
Tdrd9	T	A	12: 111,974,014 (GRCm39)		probably benign	Het
Tektl1	C	A	10: 78,586,381 (GRCm39)	L223F	probably benign	Het
Tg	T	C	15: 66,609,370 (GRCm39)	M310T	probably benign	Het
Ticam2	T	A	18: 46,693,718 (GRCm39)	D123V	probably damaging	Het
Timm23	A	G	14: 31,920,993 (GRCm39)		probably benign	Het
Tinag	C	T	9: 76,912,969 (GRCm39)	R280H	probably benign	Het
Topbp1	G	A	9: 103,186,011 (GRCm39)	R51K	probably benign	Het
Tor1b	A	G	2: 30,843,925 (GRCm39)	I121V	probably damaging	Het
Tpmt	C	A	13: 47,185,930 (GRCm39)	G148V	probably damaging	Het
Tubb1	A	G	2: 174,299,548 (GRCm39)	E410G	probably damaging	Het
Ubash3b	C	A	9: 40,958,360 (GRCm39)	V7L	possibly damaging	Het
Ube2o	C	T	11: 116,433,661 (GRCm39)	E686K	probably damaging	Het
Unc13d	T	A	11: 115,960,318 (GRCm39)		probably benign	Het
Vmn1r183	A	T	7: 23,754,601 (GRCm39)	M135L	probably benign	Het
Xkr8	T	C	4: 132,459,649 (GRCm39)	Y43C	probably damaging	Het
Zc3h4	T	A	7: 16,168,697 (GRCm39)	N935K	unknown	Het
Zc3h7a	G	A	16: 10,974,167 (GRCm39)		probably benign	Het
Zfp84	C	T	7: 29,476,276 (GRCm39)	H323Y	probably damaging	Het
Zfp873	G	T	10: 81,896,595 (GRCm39)	S442I	possibly damaging	Het
Zfp938	A	G	10: 82,061,606 (GRCm39)	L338P	probably damaging	Het

Other mutations in Atg9a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01464:Atg9a	APN	1	75,167,010 (GRCm39)	missense	probably damaging	1.00
IGL02041:Atg9a	APN	1	75,159,748 (GRCm39)	missense	possibly damaging	0.47
IGL03367:Atg9a	APN	1	75,164,601 (GRCm39)	missense	probably benign	0.18
PIT4494001:Atg9a	UTSW	1	75,164,597 (GRCm39)	nonsense	probably null
R0054:Atg9a	UTSW	1	75,161,143 (GRCm39)	missense	probably damaging	1.00
R0054:Atg9a	UTSW	1	75,161,143 (GRCm39)	missense	probably damaging	1.00
R0408:Atg9a	UTSW	1	75,161,939 (GRCm39)	missense	probably damaging	1.00
R0520:Atg9a	UTSW	1	75,163,178 (GRCm39)	nonsense	probably null
R0653:Atg9a	UTSW	1	75,166,972 (GRCm39)	missense	probably damaging	0.96
R0961:Atg9a	UTSW	1	75,163,390 (GRCm39)	missense	probably damaging	0.99
R1489:Atg9a	UTSW	1	75,162,734 (GRCm39)	missense	probably damaging	1.00
R1490:Atg9a	UTSW	1	75,162,389 (GRCm39)	missense	possibly damaging	0.70
R1692:Atg9a	UTSW	1	75,166,999 (GRCm39)	missense	probably benign	0.04
R1997:Atg9a	UTSW	1	75,166,270 (GRCm39)	missense	probably benign	0.33
R2005:Atg9a	UTSW	1	75,162,635 (GRCm39)	missense	probably benign	0.18
R2172:Atg9a	UTSW	1	75,162,329 (GRCm39)	missense	probably damaging	0.99
R4004:Atg9a	UTSW	1	75,163,095 (GRCm39)	missense	probably damaging	1.00
R4105:Atg9a	UTSW	1	75,162,603 (GRCm39)	missense	probably damaging	1.00
R5010:Atg9a	UTSW	1	75,162,704 (GRCm39)	splice site	probably null
R5220:Atg9a	UTSW	1	75,162,372 (GRCm39)	missense	probably damaging	1.00
R5898:Atg9a	UTSW	1	75,162,916 (GRCm39)	missense	probably damaging	1.00
R6295:Atg9a	UTSW	1	75,161,702 (GRCm39)	missense	probably benign	0.01
R6390:Atg9a	UTSW	1	75,164,625 (GRCm39)	missense	probably damaging	1.00
R7312:Atg9a	UTSW	1	75,164,736 (GRCm39)	missense	probably damaging	1.00
R7729:Atg9a	UTSW	1	75,161,204 (GRCm39)	missense	probably benign	0.34
R8111:Atg9a	UTSW	1	75,164,366 (GRCm39)	missense	probably damaging	1.00
R8210:Atg9a	UTSW	1	75,163,009 (GRCm39)	missense	probably damaging	1.00
R8210:Atg9a	UTSW	1	75,161,927 (GRCm39)	missense	probably damaging	1.00
R8256:Atg9a	UTSW	1	75,163,563 (GRCm39)	missense	possibly damaging	0.88
R8319:Atg9a	UTSW	1	75,162,342 (GRCm39)	nonsense	probably null
R8321:Atg9a	UTSW	1	75,162,342 (GRCm39)	nonsense	probably null
R8382:Atg9a	UTSW	1	75,162,342 (GRCm39)	nonsense	probably null
R8406:Atg9a	UTSW	1	75,167,028 (GRCm39)	missense	probably damaging	1.00
R8482:Atg9a	UTSW	1	75,162,870 (GRCm39)	missense	probably damaging	0.99
R8855:Atg9a	UTSW	1	75,161,867 (GRCm39)	missense	probably damaging	1.00
R8866:Atg9a	UTSW	1	75,161,867 (GRCm39)	missense	probably damaging	1.00
R9381:Atg9a	UTSW	1	75,162,726 (GRCm39)	missense	probably benign
R9441:Atg9a	UTSW	1	75,163,086 (GRCm39)	missense	possibly damaging	0.92
R9442:Atg9a	UTSW	1	75,163,086 (GRCm39)	missense	possibly damaging	0.92
R9448:Atg9a	UTSW	1	75,162,849 (GRCm39)	missense	probably benign	0.35
R9608:Atg9a	UTSW	1	75,161,739 (GRCm39)	missense	possibly damaging	0.52
R9703:Atg9a	UTSW	1	75,162,431 (GRCm39)	missense	probably damaging	0.98
RF021:Atg9a	UTSW	1	75,159,273 (GRCm39)	missense	probably damaging	0.96
Z1176:Atg9a	UTSW	1	75,163,203 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGAAGCAACATCAGCCCTGTGC -3'
(R):5'- GACAATGCCCTGCTATCACTGTCC -3'

Sequencing Primer
(F):5'- GATGAGCCTGCTACCACATTTG -3'
(R):5'- TATCACTGTCCTGCCGGAAG -3'

Posted On

2013-07-30