Mutagenetix > Incidental Mutation

Incidental Mutation 'R5898:Atg9a'

457621

Institutional Source

Beutler Lab

Gene Symbol

Atg9a

Ensembl Gene

ENSMUSG00000033124

Gene Name

autophagy related 9A

Synonyms

Apg9l1

MMRRC Submission

044097-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5898 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75157509-75168654 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 75162916 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 395 (T395A)

Ref Sequence

ENSEMBL: ENSMUSP00000139641 (fasta)

Gene Model

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

AlphaFold

Q68FE2

Predicted Effect

probably damaging
Transcript: ENSMUST00000040689
AA Change: T395A

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000047449
Gene: ENSMUSG00000033124
AA Change: T395A

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: T395A

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139731
Gene: ENSMUSG00000033124
AA Change: T395A

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 damaging
Transcript: ENSMUST00000189702
AA Change: T395A

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000139641
Gene: ENSMUSG00000033124
AA Change: T395A

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: T387A

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

0.4970

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.9%
20x: 93.8%

Validation Efficiency

96% (86/90)

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017N19Rik	G	T	10: 100,448,762 (GRCm39)	R158L	possibly damaging	Het
1700017N19Rik	G	A	10: 100,451,070 (GRCm39)	M179I	probably benign	Het
Abhd12	T	C	2: 150,681,698 (GRCm39)	I231V	possibly damaging	Het
Adsl	A	G	15: 80,845,554 (GRCm39)		probably null	Het
Ahnak	C	A	19: 8,991,131 (GRCm39)	N4138K	possibly damaging	Het
Ahnak	T	C	19: 8,995,575 (GRCm39)	S5620P	probably damaging	Het
Akap13	C	T	7: 75,378,894 (GRCm39)	T2145I	probably damaging	Het
Alpk2	T	A	18: 65,440,694 (GRCm39)	Q700L	probably damaging	Het
Apobec1	T	C	6: 122,557,732 (GRCm39)	Y159C	probably damaging	Het
Atp6v1f	A	G	6: 29,467,957 (GRCm39)	I48V	probably benign	Het
BC051665	A	C	13: 60,930,518 (GRCm39)	V278G	probably damaging	Het
Bicd1	A	T	6: 149,415,201 (GRCm39)	H638L	probably damaging	Het
Cacna2d4	A	G	6: 119,251,192 (GRCm39)	Y460C	probably damaging	Het
Ccdc157	C	A	11: 4,094,538 (GRCm39)	R496L	probably benign	Het
Cdcp3	T	G	7: 130,843,696 (GRCm39)		probably null	Het
Cep44	C	G	8: 56,994,056 (GRCm39)	V174L	probably damaging	Het
Clca3a1	G	T	3: 144,722,522 (GRCm39)	F283L	possibly damaging	Het
Csk	T	C	9: 57,537,585 (GRCm39)	T110A	probably benign	Het
Cspg4	T	A	9: 56,792,506 (GRCm39)		probably null	Het
Cutc	A	G	19: 43,748,468 (GRCm39)	I124V	probably benign	Het
Cyp2d9	A	G	15: 82,339,725 (GRCm39)	T104A	probably benign	Het
Cyp2j9	G	T	4: 96,465,951 (GRCm39)	T294K	probably benign	Het
D630003M21Rik	T	A	2: 158,046,577 (GRCm39)		probably null	Het
Dcaf15	G	T	8: 84,825,081 (GRCm39)	F450L	probably damaging	Het
Ddhd1	A	T	14: 45,840,125 (GRCm39)	I723K	probably damaging	Het
Dnah17	C	T	11: 118,005,039 (GRCm39)	A782T	probably benign	Het
Dnah3	T	C	7: 119,677,724 (GRCm39)	D399G	probably benign	Het
Dync2h1	T	C	9: 7,148,717 (GRCm39)	N909S	probably benign	Het
Erbin	A	G	13: 103,975,813 (GRCm39)		probably null	Het
Fanci	G	A	7: 79,083,069 (GRCm39)	V682I	probably benign	Het
Fap	A	T	2: 62,403,847 (GRCm39)	F9L	probably benign	Het
Fat3	T	C	9: 15,849,757 (GRCm39)	I3882V	probably benign	Het
Fkbp15	A	T	4: 62,244,294 (GRCm39)		probably null	Het
Fsd2	T	C	7: 81,186,975 (GRCm39)	Y601C	probably damaging	Het
Gm5900	T	C	7: 104,599,468 (GRCm39)		noncoding transcript	Het
Gramd4	G	T	15: 85,984,985 (GRCm39)	G82V	probably damaging	Het
Hc	C	T	2: 34,887,449 (GRCm39)	V1352I	probably benign	Het
Hsph1	A	T	5: 149,548,623 (GRCm39)	N466K	probably damaging	Het
Ice2	T	A	9: 69,315,544 (GRCm39)	D133E	probably benign	Het
Ifi213	T	C	1: 173,396,545 (GRCm39)	M510V	probably benign	Het
Itpkb	T	G	1: 180,248,880 (GRCm39)	L861R	probably damaging	Het
Kbtbd3	T	A	9: 4,330,476 (GRCm39)	D283E	probably damaging	Het
Man2a1	A	G	17: 64,932,375 (GRCm39)	K154R	probably benign	Het
Masp1	T	A	16: 23,310,677 (GRCm39)	I252F	probably damaging	Het
Megf11	G	T	9: 64,593,246 (GRCm39)	C586F	probably damaging	Het
Myh2	C	A	11: 67,083,545 (GRCm39)	A1476E	possibly damaging	Het
Myo18b	A	T	5: 112,950,196 (GRCm39)		probably null	Het
Naip6	A	T	13: 100,435,829 (GRCm39)	V898E	possibly damaging	Het
Nav1	T	C	1: 135,512,884 (GRCm39)	M59V	probably benign	Het
Nlrp3	A	T	11: 59,437,678 (GRCm39)	Y119F	probably benign	Het
Oxa1l	T	A	14: 54,600,758 (GRCm39)	I77N	possibly damaging	Het
Pcdhb8	T	A	18: 37,490,537 (GRCm39)	D738E	possibly damaging	Het
Pdia5	A	T	16: 35,243,335 (GRCm39)	W269R	probably damaging	Het
Peak1	T	A	9: 56,114,622 (GRCm39)	T1440S	probably benign	Het
Piezo1	A	G	8: 123,214,682 (GRCm39)	V1547A	probably benign	Het
Pkp1	T	C	1: 135,810,259 (GRCm39)	Y437C	probably damaging	Het
Pla2r1	T	C	2: 60,253,104 (GRCm39)	D1329G	probably damaging	Het
Ppip5k2	T	C	1: 97,671,887 (GRCm39)		probably benign	Het
Prrg4	C	T	2: 104,675,378 (GRCm39)	S75N	probably benign	Het
Psmb9	T	A	17: 34,401,266 (GRCm39)	I198F	probably damaging	Het
Rcbtb2	T	A	14: 73,399,405 (GRCm39)	L23*	probably null	Het
Sbno1	A	T	5: 124,524,854 (GRCm39)		probably benign	Het
Scn3a	T	C	2: 65,345,039 (GRCm39)	E483G	probably damaging	Het
Sdccag8	T	A	1: 176,652,388 (GRCm39)	D46E	probably benign	Het
Selenov	A	G	7: 27,987,579 (GRCm39)	F293L	probably damaging	Het
Septin2	A	C	1: 93,407,023 (GRCm39)	D20A	probably benign	Het
Shc1	T	A	3: 89,334,274 (GRCm39)	Y313*	probably null	Het
Siglec1	T	A	2: 130,915,553 (GRCm39)	Y1346F	probably damaging	Het
Slc22a5	T	A	11: 53,764,559 (GRCm39)	I296F	probably damaging	Het
Slc9c1	A	G	16: 45,365,123 (GRCm39)	N152S	probably damaging	Het
Smoc1	C	T	12: 81,151,531 (GRCm39)	R83*	probably null	Het
Ssx2ip	A	G	3: 146,133,586 (GRCm39)	D227G	possibly damaging	Het
Tbrg4	T	C	11: 6,567,372 (GRCm39)	D576G	probably damaging	Het
Tbx20	T	A	9: 24,670,155 (GRCm39)	Y226F	probably damaging	Het
Trav10d	G	T	14: 53,048,929 (GRCm39)	A107S	probably damaging	Het
Trim60	A	T	8: 65,453,016 (GRCm39)	L411*	probably null	Het
Ttbk2	A	T	2: 120,575,521 (GRCm39)	V1083D	probably benign	Het
Unc93a	T	A	17: 13,344,464 (GRCm39)	Q26L	probably damaging	Het
Usp14	T	A	18: 10,022,819 (GRCm39)	N65I	possibly damaging	Het
Vip	A	T	10: 5,593,988 (GRCm39)	S114C	probably damaging	Het
Vmn1r237	A	T	17: 21,534,813 (GRCm39)	I179F	probably damaging	Het
Wdr47	T	A	3: 108,545,201 (GRCm39)		probably null	Het
Zfp975	A	T	7: 42,311,963 (GRCm39)	C217S	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
R0666:Atg9a	UTSW	1	75,161,734 (GRCm39)	missense	probably damaging	0.99
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
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'- TGTGCAAGAATCACTCGGAG -3'
(R):5'- ACCTCCGCCACTTCAATGAG -3'

Sequencing Primer
(F):5'- AATCACTCGGAGCAGCTG -3'
(R):5'- CCACTTCAATGAGCTGGAGCATG -3'

Posted On

2017-02-15