Mutagenetix > Incidental Mutation

Incidental Mutation 'R8866:Atg9a'

675907

Institutional Source

Beutler Lab

Gene Symbol

Atg9a

Ensembl Gene

ENSMUSG00000033124

Gene Name

autophagy related 9A

Synonyms

Apg9l1

MMRRC Submission

068742-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8866 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

75157509-75168654 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 75161867 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Valine at position 560 (F560V)

Ref Sequence

ENSEMBL: ENSMUSP00000047449 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027396] [ENSMUST00000040689] [ENSMUST00000186744] [ENSMUST00000188347] [ENSMUST00000189665] [ENSMUST00000189702]

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: F560V

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

SMART Domains

Protein: ENSMUSP00000047449
Gene: ENSMUSG00000033124
AA Change: F560V

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

probably benign
Transcript: ENSMUST00000186744

Predicted Effect

probably damaging
Transcript: ENSMUST00000188347
AA Change: F560V

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

SMART Domains

Protein: ENSMUSP00000139731
Gene: ENSMUSG00000033124
AA Change: F560V

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 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: F560V

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

SMART Domains

Protein: ENSMUSP00000139641
Gene: ENSMUSG00000033124
AA Change: F560V

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl2	C	T	3: 59,914,511 (GRCm39)	T38I	probably benign	Het
Arhgap1	G	T	2: 91,499,744 (GRCm39)	S293I	probably benign	Het
Arhgap45	C	A	10: 79,853,750 (GRCm39)	P88Q	probably damaging	Het
Btaf1	T	A	19: 36,935,901 (GRCm39)	N230K	probably benign	Het
Ccne1	A	C	7: 37,800,046 (GRCm39)	H179Q	probably benign	Het
Dbr1	T	A	9: 99,460,497 (GRCm39)	L109*	probably null	Het
Dchs1	G	T	7: 105,404,597 (GRCm39)	N2648K	probably benign	Het
Ddx47	A	G	6: 135,000,356 (GRCm39)	K451E	probably benign	Het
Dlgap1	A	T	17: 70,823,435 (GRCm39)	H140L	probably damaging	Het
Dnah11	T	A	12: 118,156,107 (GRCm39)	H181L	probably benign	Het
Dync1h1	T	C	12: 110,602,333 (GRCm39)	C2074R	probably damaging	Het
Ell2	A	T	13: 75,917,793 (GRCm39)	Q574H	probably damaging	Het
Eloa	A	C	4: 135,737,538 (GRCm39)		probably null	Het
Epha7	A	G	4: 28,821,614 (GRCm39)	I260V	probably benign	Het
Fbp2	T	C	13: 62,989,709 (GRCm39)	K199R	probably benign	Het
Fetub	A	T	16: 22,758,321 (GRCm39)	E368V	possibly damaging	Het
Fsip2	A	G	2: 82,810,521 (GRCm39)	Q2280R	probably benign	Het
Fstl4	A	G	11: 52,963,233 (GRCm39)	E205G	possibly damaging	Het
Gm5592	A	T	7: 40,938,246 (GRCm39)	R509S	possibly damaging	Het
Gpld1	A	G	13: 25,170,890 (GRCm39)	T794A	probably benign	Het
Gsk3b	A	G	16: 38,004,900 (GRCm39)	Y157C	probably damaging	Het
Hgs	A	G	11: 120,360,464 (GRCm39)	N54S	probably benign	Het
Hydin	G	A	8: 111,308,779 (GRCm39)	V4022M	possibly damaging	Het
Kank1	T	C	19: 25,388,702 (GRCm39)	S792P	possibly damaging	Het
Kctd4	A	G	14: 76,200,465 (GRCm39)	I145M	probably benign	Het
Klra5	A	T	6: 129,880,533 (GRCm39)	W212R	probably damaging	Het
Lrp6	A	T	6: 134,445,785 (GRCm39)	N1009K	probably benign	Het
Lrrc10	T	A	10: 116,881,858 (GRCm39)	N177K	probably damaging	Het
Lrrc39	T	A	3: 116,363,790 (GRCm39)	I121N	probably damaging	Het
Mov10l1	A	T	15: 88,896,169 (GRCm39)	D671V	probably benign	Het
Ndel1	A	G	11: 68,734,645 (GRCm39)		probably null	Het
Or10g3	A	T	14: 52,610,196 (GRCm39)	Y105N	probably damaging	Het
Or1e27-ps1	A	G	11: 73,555,825 (GRCm39)	Y130C	probably damaging	Het
Or1e32	A	T	11: 73,705,237 (GRCm39)	S224T	probably damaging	Het
Or51a43	A	T	7: 103,718,119 (GRCm39)	S40T	probably damaging	Het
Otop2	A	G	11: 115,220,354 (GRCm39)	D398G	probably benign	Het
Pkd1	T	C	17: 24,792,051 (GRCm39)	V1246A	probably damaging	Het
Polr3b	T	A	10: 84,531,555 (GRCm39)	D810E	probably benign	Het
Ppl	T	A	16: 4,920,211 (GRCm39)	T395S	probably benign	Het
Ptprm	G	A	17: 67,116,630 (GRCm39)	A883V	probably benign	Het
Rapgef6	G	A	11: 54,443,700 (GRCm39)		probably null	Het
Rbm12	A	T	2: 155,938,693 (GRCm39)	Y526*	probably null	Het
Rbm15b	C	T	9: 106,763,595 (GRCm39)	R191Q	probably benign	Het
Rsf1	GCGGCGGCG	GCGGCGGCGACGGCGGCG	7: 97,229,120 (GRCm39)		probably benign	Het
Rxylt1	A	G	10: 121,924,953 (GRCm39)	Y250H	probably damaging	Het
Serpinb6c	A	T	13: 34,083,309 (GRCm39)	I35N	probably damaging	Het
Setd4	A	G	16: 93,386,961 (GRCm39)	F246L	probably damaging	Het
Shank2	A	G	7: 143,964,986 (GRCm39)	S865G	probably benign	Het
Skint6	T	C	4: 112,711,650 (GRCm39)	N956D	probably benign	Het
Slc30a3	C	A	5: 31,245,325 (GRCm39)	V332F	possibly damaging	Het
Smg1	A	G	7: 117,806,122 (GRCm39)	S240P	unknown	Het
Tank	T	A	2: 61,409,005 (GRCm39)	S7R	probably benign	Het
Tecpr1	T	C	5: 144,153,117 (GRCm39)	E204G	possibly damaging	Het
Tmem74	A	G	15: 43,730,231 (GRCm39)	S271P	probably damaging	Het
Tor4a	T	C	2: 25,084,965 (GRCm39)	M313V	probably benign	Het
Tpd52l2	A	G	2: 181,154,861 (GRCm39)	D192G	probably damaging	Het
Trim29	T	C	9: 43,222,945 (GRCm39)	V258A	probably damaging	Het
Ttc39c	A	T	18: 12,831,003 (GRCm39)	S288C	probably benign	Het
Ttn	T	C	2: 76,592,675 (GRCm39)	E20819G	probably damaging	Het
Twnk	C	T	19: 45,000,272 (GRCm39)	Q663*	probably null	Het
Ucn	T	A	5: 31,295,857 (GRCm39)	Q3L	probably benign	Het
Unc80	G	A	1: 66,629,388 (GRCm39)	G1295E	probably benign	Het
Usp9y	C	T	Y: 1,395,758 (GRCm39)	R492H	probably damaging	Het
Vars1	T	C	17: 35,234,620 (GRCm39)	S1150P	probably benign	Het
Vwa5b1	T	G	4: 138,327,628 (GRCm39)	E316A	probably damaging	Het
Zc3h7b	G	A	15: 81,656,681 (GRCm39)	R166Q	probably benign	Het
Zfp839	A	G	12: 110,834,848 (GRCm39)	E701G	probably benign	Het
Zfp931	A	T	2: 177,710,178 (GRCm39)	C69*	probably null	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
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
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'- ACCTCGGACTCAGACTGTAAG -3'
(R):5'- GTACAGTTCAAGTGACTGACCCAG -3'

Sequencing Primer
(F):5'- CTCGGACTCAGACTGTAAGGACTG -3'
(R):5'- TCAAGTGACTGACCCAGTATGTG -3'

Posted On

2021-07-15