Mutagenetix > Incidental Mutation

Incidental Mutation 'R5470:Atp6v1d'

433485

Institutional Source

Beutler Lab

Gene Symbol

Atp6v1d

Ensembl Gene

ENSMUSG00000021114

Gene Name

ATPase, H+ transporting, lysosomal V1 subunit D

Synonyms

1110004P10Rik, lysosomal 34kDa, Atp6m, Vma8, VATD

MMRRC Submission

043031-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5470 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

78889756-78908810 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 78892058 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 182 (R182C)

Ref Sequence

ENSEMBL: ENSMUSP00000021536 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021536] [ENSMUST00000082024] [ENSMUST00000219197]

AlphaFold

P57746

Predicted Effect

probably benign
Transcript: ENSMUST00000021536
AA Change: R182C

PolyPhen 2 Score 0.423 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000021536
Gene: ENSMUSG00000021114
AA Change: R182C

Domain	Start	End	E-Value	Type
Pfam:ATP-synt_D	15	207	1.2e-76	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000082024

SMART Domains

Protein: ENSMUSP00000080683
Gene: ENSMUSG00000021112

Domain	Start	End	E-Value	Type
coiled coil region	54	76	N/A	INTRINSIC
L27	123	180	2.04e-10	SMART
L27	186	238	7.39e-8	SMART
PDZ	265	336	5.99e-13	SMART
SH3	348	416	1.2e-10	SMART
low complexity region	439	454	N/A	INTRINSIC
GuKc	478	663	1.72e-64	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000219197

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219316

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219377

Meta Mutation Damage Score

0.1763

Coding Region Coverage

1x: 98.3%
3x: 97.3%
10x: 95.1%
20x: 90.4%

Validation Efficiency

99% (79/80)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c", and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This gene encodes the V1 domain D subunit protein. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actn1	T	A	12: 80,215,715 (GRCm39)	I813F	probably damaging	Het
Aqr	G	A	2: 113,988,056 (GRCm39)	L169F	probably damaging	Het
Bcl2l13	G	T	6: 120,839,833 (GRCm39)	A44S	probably benign	Het
Brip1	T	C	11: 86,039,368 (GRCm39)	K389E	possibly damaging	Het
C530025M09Rik	G	A	2: 149,673,045 (GRCm39)		probably benign	Het
Ccdc7b	T	A	8: 129,799,081 (GRCm39)	S53T	possibly damaging	Het
Chd8	A	G	14: 52,450,066 (GRCm39)	F154L	probably damaging	Het
Cop1	A	T	1: 159,094,430 (GRCm39)		probably benign	Het
Cyp2c39	A	G	19: 39,501,974 (GRCm39)	K121R	possibly damaging	Het
Cyp3a57	A	G	5: 145,309,429 (GRCm39)	M256V	probably benign	Het
Deup1	T	C	9: 15,493,916 (GRCm39)		probably null	Het
Dnah10	A	G	5: 124,830,232 (GRCm39)	N709D	probably benign	Het
Dthd1	A	G	5: 62,976,109 (GRCm39)	Y261C	probably damaging	Het
Ear-ps2	G	A	14: 44,284,517 (GRCm39)		noncoding transcript	Het
En2	C	T	5: 28,371,922 (GRCm39)	T133M	probably benign	Het
Endou	A	G	15: 97,616,836 (GRCm39)	F229S	probably damaging	Het
Etl4	A	T	2: 20,534,791 (GRCm39)	H79L	probably damaging	Het
Fah	C	T	7: 84,242,393 (GRCm39)		probably null	Het
Fetub	C	T	16: 22,751,081 (GRCm39)	R143C	probably damaging	Het
Fignl1	T	A	11: 11,752,640 (GRCm39)	E138D	probably benign	Het
Fndc3a	A	G	14: 72,812,008 (GRCm39)	L311P	possibly damaging	Het
Gdf9	T	A	11: 53,327,581 (GRCm39)	V179E	probably benign	Het
Gm14129	G	T	2: 148,769,737 (GRCm39)		noncoding transcript	Het
Gorab	A	G	1: 163,220,078 (GRCm39)	I188T	probably damaging	Het
Gpr152	G	A	19: 4,193,128 (GRCm39)	C223Y	probably damaging	Het
Heatr5b	A	T	17: 79,129,008 (GRCm39)		probably null	Het
Hsd17b3	G	T	13: 64,221,713 (GRCm39)	T104N	probably damaging	Het
Il6ra	C	T	3: 89,793,302 (GRCm39)	V283M	probably benign	Het
Klk1b16	A	T	7: 43,786,755 (GRCm39)	I5F	probably damaging	Het
Krt74	G	A	15: 101,662,900 (GRCm39)		noncoding transcript	Het
Lrch3	T	A	16: 32,818,960 (GRCm39)	N650K	probably damaging	Het
Ly96	A	T	1: 16,779,710 (GRCm39)	E126D	probably benign	Het
Mgarp	C	A	3: 51,298,706 (GRCm39)	R66L	possibly damaging	Het
Naalad2	T	A	9: 18,242,147 (GRCm39)	T586S	probably damaging	Het
Ndufaf3	T	C	9: 108,443,643 (GRCm39)		probably benign	Het
Neb	A	G	2: 52,139,450 (GRCm39)	M3055T	possibly damaging	Het
Neo1	G	T	9: 58,838,350 (GRCm39)	A478D	probably damaging	Het
Nmrk1	A	T	19: 18,617,248 (GRCm39)		probably null	Het
Nsl1	T	C	1: 190,812,737 (GRCm39)	M184T	probably benign	Het
Nup133	T	C	8: 124,657,705 (GRCm39)	N410S	probably benign	Het
Opalin	A	G	19: 41,054,970 (GRCm39)	S75P	probably benign	Het
Or1e17	T	C	11: 73,831,696 (GRCm39)	I208T	probably benign	Het
Or3a4	A	G	11: 73,944,733 (GRCm39)	I284T	possibly damaging	Het
Or51ag1	T	G	7: 103,155,716 (GRCm39)	I146L	probably benign	Het
Palb2	C	A	7: 121,713,574 (GRCm39)	C903F	probably damaging	Het
Pcm1	T	A	8: 41,740,720 (GRCm39)	W989R	probably damaging	Het
Pfkfb4	T	A	9: 108,856,661 (GRCm39)	I389N	probably damaging	Het
Pitrm1	T	C	13: 6,603,306 (GRCm39)	C119R	probably benign	Het
Plekha1	T	C	7: 130,510,106 (GRCm39)	V45A	probably damaging	Het
Pold2	G	A	11: 5,823,048 (GRCm39)	P376S	probably damaging	Het
Rcan2	A	G	17: 44,147,174 (GRCm39)	D4G	probably benign	Het
Slc12a1	A	T	2: 125,012,634 (GRCm39)	T299S	probably damaging	Het
Slc22a29	A	T	19: 8,138,880 (GRCm39)	H527Q	probably benign	Het
Slc22a8	G	A	19: 8,585,234 (GRCm39)	R261H	probably damaging	Het
Slc35e2	C	T	4: 155,694,483 (GRCm39)	P10L	probably benign	Het
Slco4a1	T	C	2: 180,115,907 (GRCm39)	F681S	probably benign	Het
Sorcs2	A	T	5: 36,188,527 (GRCm39)	H860Q	probably benign	Het
Strn	A	T	17: 78,964,374 (GRCm39)	H530Q	probably benign	Het
Tex14	A	G	11: 87,442,430 (GRCm39)	R179G	probably damaging	Het
Tjp3	T	C	10: 81,115,381 (GRCm39)	D350G	probably benign	Het
Tnrc6b	G	T	15: 80,800,912 (GRCm39)	R1406L	possibly damaging	Het
Tnxb	A	G	17: 34,935,947 (GRCm39)	D2666G	probably null	Het
Ttn	A	T	2: 76,560,208 (GRCm39)	Y27652N	probably benign	Het
Utp20	T	A	10: 88,653,758 (GRCm39)	E287D	probably benign	Het
Vmn1r45	T	C	6: 89,910,698 (GRCm39)	I91V	probably benign	Het
Wdr72	A	T	9: 74,046,981 (GRCm39)	K76*	probably null	Het
Zfp689	C	T	7: 127,043,425 (GRCm39)	A402T	probably damaging	Het
Zfpm1	A	G	8: 123,060,532 (GRCm39)	E207G	probably damaging	Het
Zhx2	G	T	15: 57,686,470 (GRCm39)	R613L	possibly damaging	Het

Other mutations in Atp6v1d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00709:Atp6v1d	APN	12	78,896,528 (GRCm39)	missense	probably benign
IGL02319:Atp6v1d	APN	12	78,908,230 (GRCm39)	missense	probably damaging	1.00
IGL03037:Atp6v1d	APN	12	78,904,122 (GRCm39)	unclassified	probably benign
IGL03040:Atp6v1d	APN	12	78,904,122 (GRCm39)	unclassified	probably benign
R1015:Atp6v1d	UTSW	12	78,896,543 (GRCm39)	missense	possibly damaging	0.70
R1203:Atp6v1d	UTSW	12	78,908,214 (GRCm39)	missense	possibly damaging	0.88
R8479:Atp6v1d	UTSW	12	78,896,520 (GRCm39)	missense	probably benign
R9252:Atp6v1d	UTSW	12	78,904,023 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- ACCAACTGTGCTTATTCCAAAG -3'
(R):5'- CTGTTTTGACCCAATATGGTATCTG -3'

Sequencing Primer
(F):5'- CTGTGCTTATTCCAAAGTTCATTAAG -3'
(R):5'- TGACCCAATATGGTATCTGTACATAG -3'

Posted On

2016-10-06