Mutagenetix > Incidental Mutation

Incidental Mutation 'G5030:Atp13a4'

488

Institutional Source

Beutler Lab

Gene Symbol

Atp13a4

Ensembl Gene

ENSMUSG00000038094

Gene Name

ATPase type 13A4

Synonyms

4631413J11Rik, 9330174J19Rik

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

G5030 (G3) of strain 560

Quality Score

Status

Validated

Chromosome

Chromosomal Location

29214671-29363682 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 29274306 bp (GRCm39)

Zygosity

Homozygous

Amino Acid Change

Isoleucine to Threonine at position 385 (I385T)

Ref Sequence

ENSEMBL: ENSMUSP00000048753 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039090] [ENSMUST00000057018] [ENSMUST00000182013] [ENSMUST00000182627]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000039090
AA Change: I385T

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

SMART Domains

Protein: ENSMUSP00000048753
Gene: ENSMUSG00000038094
AA Change: I385T

Domain	Start	End	E-Value	Type
Pfam:P5-ATPase	17	143	8.4e-31	PFAM
Cation_ATPase_N	147	223	1.09e-1	SMART
Pfam:E1-E2_ATPase	229	476	1.7e-36	PFAM
Pfam:Hydrolase	481	769	3.9e-11	PFAM
Pfam:HAD	484	787	4.1e-14	PFAM
Pfam:Hydrolase_like2	574	637	1.2e-9	PFAM
transmembrane domain	824	846	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000057018
AA Change: I385T

SMART Domains

Protein: ENSMUSP00000060987
Gene: ENSMUSG00000038094
AA Change: I385T

Domain	Start	End	E-Value	Type
Pfam:P5-ATPase	17	142	9.6e-34	PFAM
Cation_ATPase_N	147	223	1.09e-1	SMART
Pfam:E1-E2_ATPase	228	476	1.6e-34	PFAM
Pfam:Hydrolase	481	767	1.1e-10	PFAM
Pfam:HAD	484	858	3.3e-23	PFAM
Pfam:Cation_ATPase	573	637	4.9e-8	PFAM
transmembrane domain	902	924	N/A	INTRINSIC
transmembrane domain	934	951	N/A	INTRINSIC
transmembrane domain	972	994	N/A	INTRINSIC
low complexity region	1014	1023	N/A	INTRINSIC
transmembrane domain	1040	1057	N/A	INTRINSIC
transmembrane domain	1070	1092	N/A	INTRINSIC
transmembrane domain	1107	1126	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000182013

SMART Domains

Protein: ENSMUSP00000138583
Gene: ENSMUSG00000038094

Domain	Start	End	E-Value	Type
Pfam:P5-ATPase	17	84	4.2e-26	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000182573
AA Change: I23T

Predicted Effect

probably damaging
Transcript: ENSMUST00000182627
AA Change: I385T

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000138479
Gene: ENSMUSG00000038094
AA Change: I385T

Domain	Start	End	E-Value	Type
Pfam:P5-ATPase	17	143	2.1e-29	PFAM
Cation_ATPase_N	147	223	1.09e-1	SMART
Pfam:E1-E2_ATPase	229	476	3.9e-35	PFAM
Pfam:Hydrolase	481	861	4.2e-16	PFAM
Pfam:HAD	484	858	1.9e-23	PFAM
Pfam:Hydrolase_like2	574	637	2.2e-8	PFAM
transmembrane domain	902	924	N/A	INTRINSIC
transmembrane domain	934	951	N/A	INTRINSIC
transmembrane domain	972	994	N/A	INTRINSIC
low complexity region	1014	1023	N/A	INTRINSIC
transmembrane domain	1040	1057	N/A	INTRINSIC
transmembrane domain	1070	1092	N/A	INTRINSIC
transmembrane domain	1107	1126	N/A	INTRINSIC

Meta Mutation Damage Score

0.5676

Coding Region Coverage

1x: 81.1%
3x: 60.2%

Het Detection Efficiency

35.6%

Validation Efficiency

87% (206/237)

Allele List at MGI

Other mutations in this stock

Total: 30 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8a	T	A	11: 109,961,165 (GRCm39)	I585F	probably damaging	Het
Adam18	C	G	8: 25,141,872 (GRCm39)	L232F	probably benign	Homo
Ccdc17	T	A	4: 116,455,699 (GRCm39)	S277T	probably benign	Het
Ccng1	A	G	11: 40,644,629 (GRCm39)		probably benign	Het
Ces1f	T	C	8: 94,000,847 (GRCm39)	D99G	probably benign	Het
Clec16a	G	A	16: 10,389,425 (GRCm39)	R187Q	probably damaging	Homo
Cryl1	C	T	14: 57,579,595 (GRCm39)		probably benign	Het
Cryzl2	C	T	1: 157,292,580 (GRCm39)	Q48*	probably null	Het
Dtx4	A	G	19: 12,446,943 (GRCm39)	L583P	probably benign	Het
Ephx4	A	T	5: 107,577,693 (GRCm39)	D339V	probably damaging	Het
Eri2	A	T	7: 119,385,601 (GRCm39)	V300E	possibly damaging	Het
F3	T	A	3: 121,518,648 (GRCm39)	N37K	probably damaging	Homo
Fpr1	A	T	17: 18,097,068 (GRCm39)	L307H	probably damaging	Het
Fv1	T	A	4: 147,953,618 (GRCm39)	N61K	possibly damaging	Het
Gm5548	T	C	3: 112,961,512 (GRCm39)		noncoding transcript	Homo
Il1r1	A	G	1: 40,352,323 (GRCm39)	K498E	possibly damaging	Homo
Myh11	T	C	16: 14,068,443 (GRCm39)	I192M	probably damaging	Homo
Nckap5	T	C	1: 125,953,591 (GRCm39)	K923R	probably damaging	Het
Nmbr	A	T	10: 14,642,747 (GRCm39)	Y102F	possibly damaging	Het
Or6c75	A	G	10: 129,337,406 (GRCm39)	T218A	probably benign	Homo
Pde1a	C	T	2: 79,718,180 (GRCm39)		probably benign	Het
Pex6	T	C	17: 47,026,382 (GRCm39)		probably benign	Het
Rtn2	T	C	7: 19,027,099 (GRCm39)	S305P	probably damaging	Homo
Saal1	G	A	7: 46,342,207 (GRCm39)	T412I	probably damaging	Homo
Slc46a2	A	T	4: 59,913,867 (GRCm39)	I352N	probably damaging	Het
Trim37	A	T	11: 87,033,967 (GRCm39)	H99L	probably damaging	Het
Tubgcp4	C	T	2: 121,014,815 (GRCm39)	R242C	probably damaging	Het
Twf2	C	A	9: 106,084,141 (GRCm39)	L27I	possibly damaging	Het
Usp40	A	T	1: 87,921,941 (GRCm39)	H307Q	probably damaging	Het
Zfhx3	T	G	8: 109,678,091 (GRCm39)	V3047G	possibly damaging	Het

Other mutations in Atp13a4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00563:Atp13a4	APN	16	29,222,596 (GRCm39)	splice site	probably benign
IGL01577:Atp13a4	APN	16	29,260,102 (GRCm39)	missense	possibly damaging	0.77
IGL01834:Atp13a4	APN	16	29,234,595 (GRCm39)	splice site	probably benign
IGL02165:Atp13a4	APN	16	29,252,828 (GRCm39)	missense	probably damaging	1.00
IGL02194:Atp13a4	APN	16	29,275,447 (GRCm39)	missense	probably damaging	1.00
IGL02322:Atp13a4	APN	16	29,258,920 (GRCm39)	missense	probably benign	0.00
IGL02553:Atp13a4	APN	16	29,241,521 (GRCm39)	missense	probably benign	0.03
IGL02821:Atp13a4	APN	16	29,260,125 (GRCm39)	missense	probably benign	0.01
IGL03349:Atp13a4	APN	16	29,275,489 (GRCm39)	missense	probably benign	0.01
R0091:Atp13a4	UTSW	16	29,274,213 (GRCm39)	missense	probably damaging	1.00
R0100:Atp13a4	UTSW	16	29,240,542 (GRCm39)	missense	probably damaging	1.00
R0278:Atp13a4	UTSW	16	29,273,652 (GRCm39)	missense	probably damaging	1.00
R1263:Atp13a4	UTSW	16	29,290,771 (GRCm39)	missense	possibly damaging	0.60
R1378:Atp13a4	UTSW	16	29,239,246 (GRCm39)	missense	probably damaging	1.00
R1575:Atp13a4	UTSW	16	29,228,528 (GRCm39)	missense	probably benign	0.01
R1720:Atp13a4	UTSW	16	29,227,746 (GRCm39)	missense	probably damaging	0.99
R1759:Atp13a4	UTSW	16	29,275,429 (GRCm39)	missense	probably damaging	0.99
R1967:Atp13a4	UTSW	16	29,298,672 (GRCm39)	missense	probably damaging	0.99
R2030:Atp13a4	UTSW	16	29,241,502 (GRCm39)	missense	probably damaging	1.00
R2113:Atp13a4	UTSW	16	29,260,102 (GRCm39)	missense	possibly damaging	0.77
R3409:Atp13a4	UTSW	16	29,232,567 (GRCm39)	missense	probably damaging	1.00
R3410:Atp13a4	UTSW	16	29,232,567 (GRCm39)	missense	probably damaging	1.00
R4032:Atp13a4	UTSW	16	29,237,389 (GRCm39)	missense	probably damaging	1.00
R4163:Atp13a4	UTSW	16	29,360,068 (GRCm39)	missense	possibly damaging	0.87
R4652:Atp13a4	UTSW	16	29,271,421 (GRCm39)	missense	probably damaging	1.00
R4772:Atp13a4	UTSW	16	29,239,653 (GRCm39)	intron	probably benign
R4795:Atp13a4	UTSW	16	29,308,826 (GRCm39)	critical splice donor site	probably null
R4898:Atp13a4	UTSW	16	29,227,779 (GRCm39)	nonsense	probably null
R4996:Atp13a4	UTSW	16	29,290,822 (GRCm39)	missense	probably damaging	1.00
R5112:Atp13a4	UTSW	16	29,228,686 (GRCm39)	missense	possibly damaging	0.87
R5259:Atp13a4	UTSW	16	29,275,428 (GRCm39)	missense	probably damaging	1.00
R5395:Atp13a4	UTSW	16	29,275,422 (GRCm39)	missense	possibly damaging	0.94
R5395:Atp13a4	UTSW	16	29,239,706 (GRCm39)	nonsense	probably null
R5640:Atp13a4	UTSW	16	29,234,649 (GRCm39)	missense	probably damaging	0.98
R5809:Atp13a4	UTSW	16	29,252,805 (GRCm39)	missense	possibly damaging	0.56
R5856:Atp13a4	UTSW	16	29,252,805 (GRCm39)	missense	possibly damaging	0.94
R5912:Atp13a4	UTSW	16	29,275,389 (GRCm39)	missense	probably benign	0.33
R6282:Atp13a4	UTSW	16	29,252,822 (GRCm39)	missense	probably benign	0.00
R6404:Atp13a4	UTSW	16	29,290,719 (GRCm39)	nonsense	probably null
R6497:Atp13a4	UTSW	16	29,298,719 (GRCm39)	missense	probably damaging	1.00
R6577:Atp13a4	UTSW	16	29,298,659 (GRCm39)	missense	probably benign	0.03
R6806:Atp13a4	UTSW	16	29,288,098 (GRCm39)	missense	probably damaging	1.00
R7229:Atp13a4	UTSW	16	29,239,723 (GRCm39)	missense	probably benign	0.05
R7438:Atp13a4	UTSW	16	29,260,014 (GRCm39)	missense
R7493:Atp13a4	UTSW	16	29,290,774 (GRCm39)	missense
R7712:Atp13a4	UTSW	16	29,278,305 (GRCm39)	missense
R7739:Atp13a4	UTSW	16	29,275,419 (GRCm39)	missense
R7897:Atp13a4	UTSW	16	29,215,284 (GRCm39)	missense
R7950:Atp13a4	UTSW	16	29,268,735 (GRCm39)	missense
R8217:Atp13a4	UTSW	16	29,222,619 (GRCm39)	missense
R8227:Atp13a4	UTSW	16	29,222,663 (GRCm39)	missense
R8273:Atp13a4	UTSW	16	29,290,720 (GRCm39)	missense
R8488:Atp13a4	UTSW	16	29,236,654 (GRCm39)	missense	possibly damaging	0.63
R8508:Atp13a4	UTSW	16	29,273,587 (GRCm39)	nonsense	probably null
R8773:Atp13a4	UTSW	16	29,260,398 (GRCm39)	missense
R8921:Atp13a4	UTSW	16	29,273,592 (GRCm39)	missense
R8940:Atp13a4	UTSW	16	29,273,508 (GRCm39)	critical splice donor site	probably null
R9056:Atp13a4	UTSW	16	29,290,706 (GRCm39)	critical splice donor site	probably null
R9272:Atp13a4	UTSW	16	29,268,797 (GRCm39)	missense
R9292:Atp13a4	UTSW	16	29,241,500 (GRCm39)	missense
R9415:Atp13a4	UTSW	16	29,227,821 (GRCm39)	missense
R9453:Atp13a4	UTSW	16	29,239,659 (GRCm39)	missense	unknown
R9497:Atp13a4	UTSW	16	29,288,130 (GRCm39)	critical splice acceptor site	probably null
R9541:Atp13a4	UTSW	16	29,241,544 (GRCm39)	missense
R9614:Atp13a4	UTSW	16	29,260,398 (GRCm39)	missense
R9622:Atp13a4	UTSW	16	29,239,277 (GRCm39)	missense
R9727:Atp13a4	UTSW	16	29,228,589 (GRCm39)	missense
Z1176:Atp13a4	UTSW	16	29,241,405 (GRCm39)	missense	probably null

Nature of Mutation

DNA sequencing using the SOLiD technique identified a T to C transition at position 1331 of the Atp13a4 transcript using Genbank record NM_001164612. Two transcripts of the Atp13a4 gene are displayed on Ensembl. The mutated nucleotide causes an isoleucine to threonine substitution at amino acid 385 of the encoded protein. The mutation has been confirmed by DNA sequencing using the Sanger method (Figure 1).

Protein Function and Prediction

The Atp13a4 gene encodes multiple isoforms with isoform 1 containing 1193 amino acids. The protein is a ten-pass transmembrane protein belonging to the cation transport ATPase (P-type) family in the type V subfamily (Uniprot Q5XF90). ATP13A4 contains a cation ATPase domain (amino acids 146–222), an E1–E2 ATPase domain (amino acids 229–477), and a hydrolase domain (amino acids 713– 870). Highly conserved regions in ATP13A4 include: the E1–E2 ATPase phosphorylation site CFDKTGTLT (amino acids 485–493), the phosphatase site LTGES (amino acids 314–318), and the nucleotide-binding domain KGA(S)PE (amino acids 625–629). ATP13A4 also contains the PPxxP motif (amino acids 444–448), a characteristic feature of the P₅ ATPases.

The I385T change is located in the E1–E2 ATPase domain, and is predicted to be probably damaging by the PolyPhen program.

Posted On

2010-10-27