Mutagenetix > Incidental Mutation

Incidental Mutation 'R2437:Rab3d'

249660

Institutional Source

Beutler Lab

Gene Symbol

Rab3d

Ensembl Gene

ENSMUSG00000019066

Gene Name

RAB3D, member RAS oncogene family

Synonyms

C130057E11Rik

MMRRC Submission

040398-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2437 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

21818787-21829488 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 21827147 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 28 (I28V)

Ref Sequence

ENSEMBL: ENSMUSP00000113322 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000115351] [ENSMUST00000119055] [ENSMUST00000122211] [ENSMUST00000128442]

AlphaFold

P35276

Predicted Effect

probably damaging
Transcript: ENSMUST00000115351
AA Change: I28V

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000111008
Gene: ENSMUSG00000019066
AA Change: I28V

Domain	Start	End	E-Value	Type
RAB	23	186	1.23e-96	SMART
low complexity region	193	204	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000119055
AA Change: I28V

PolyPhen 2 Score 0.135 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000114106
Gene: ENSMUSG00000019066
AA Change: I28V

Domain	Start	End	E-Value	Type
Pfam:Arf	14	130	3e-11	PFAM
Pfam:Gtr1_RagA	24	126	2.3e-7	PFAM
Pfam:Miro	24	128	2.2e-15	PFAM
Pfam:Ras	24	130	6.6e-40	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000122211
AA Change: I28V

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000113322
Gene: ENSMUSG00000019066
AA Change: I28V

Domain	Start	End	E-Value	Type
RAB	23	186	1.23e-96	SMART
low complexity region	193	204	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000128442
AA Change: I28V

PolyPhen 2 Score 0.299 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000120067
Gene: ENSMUSG00000019066
AA Change: I28V

Domain	Start	End	E-Value	Type
Pfam:Arf	14	106	1.5e-9	PFAM
Pfam:Gtr1_RagA	24	96	1.7e-6	PFAM
Pfam:Miro	24	106	1.4e-11	PFAM
Pfam:Ras	24	106	1.3e-33	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154019

Meta Mutation Damage Score

0.1624

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.0%
20x: 94.0%

Validation Efficiency

100% (75/75)

MGI Phenotype

PHENOTYPE: Mice homozygous for disruptions in this gene show no obvious phenotypic changes. Secretory granules in mast cells and some exocrine glands are double in volume however. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510039O18Rik	A	G	4: 148,031,075 (GRCm39)	*635W	probably null	Het
Anxa2	A	G	9: 69,397,046 (GRCm39)	Y317C	probably damaging	Het
Arhgef26	T	C	3: 62,340,002 (GRCm39)	S675P	probably damaging	Het
Bltp1	T	A	3: 37,012,834 (GRCm39)		probably null	Het
Camk2d	A	G	3: 126,628,277 (GRCm39)	N53S	probably damaging	Het
Carns1	A	T	19: 4,215,782 (GRCm39)	M800K	possibly damaging	Het
Ces1f	A	T	8: 93,996,767 (GRCm39)		probably null	Het
Chrne	T	A	11: 70,506,086 (GRCm39)	D426V	possibly damaging	Het
Cntfr	T	C	4: 41,671,035 (GRCm39)	T43A	probably damaging	Het
Cntn5	A	T	9: 10,048,758 (GRCm39)	C63*	probably null	Het
Col12a1	G	A	9: 79,599,501 (GRCm39)	T884I	probably damaging	Het
Dnah5	T	C	15: 28,307,537 (GRCm39)		probably null	Het
Dnajc2	A	T	5: 21,965,389 (GRCm39)	S537R	probably benign	Het
Dnajc25	T	C	4: 59,020,234 (GRCm39)	I100T	probably damaging	Het
Ephx1	C	A	1: 180,823,661 (GRCm39)	G149C	probably damaging	Het
Fam163b	G	T	2: 27,002,698 (GRCm39)	P100T	probably damaging	Het
Fbxl9	A	G	8: 106,039,675 (GRCm39)		probably null	Het
Fgd5	A	T	6: 92,039,850 (GRCm39)	R1017*	probably null	Het
Fibin	A	T	2: 110,192,848 (GRCm39)	L98Q	probably damaging	Het
Fndc3b	A	T	3: 27,505,481 (GRCm39)	L929H	probably damaging	Het
Frem1	T	A	4: 82,918,410 (GRCm39)	S512C	probably damaging	Het
Gm4922	T	A	10: 18,659,829 (GRCm39)	M298L	probably benign	Het
Gstm2	G	A	3: 107,891,369 (GRCm39)		probably benign	Het
Gtf3c2	A	G	5: 31,317,042 (GRCm39)		probably null	Het
Ibtk	A	C	9: 85,590,178 (GRCm39)	L1026V	probably benign	Het
Il9	T	A	13: 56,629,684 (GRCm39)		probably benign	Het
Inpp4a	T	C	1: 37,432,037 (GRCm39)	S146P	probably damaging	Het
Kcnab1	G	T	3: 65,264,435 (GRCm39)		probably benign	Het
Mgat4c	T	C	10: 102,224,436 (GRCm39)	S217P	probably damaging	Het
Mr1	T	C	1: 155,008,277 (GRCm39)	M233V	probably benign	Het
Ncoa2	G	A	1: 13,218,584 (GRCm39)	T1415I	probably damaging	Het
Oasl2	G	A	5: 115,049,357 (GRCm39)	D486N	probably benign	Het
Or1j14	A	T	2: 36,418,258 (GRCm39)	Y278F	probably damaging	Het
Or9a7	G	A	6: 40,521,856 (GRCm39)	T19I	probably benign	Het
Or9s27	T	C	1: 92,516,688 (GRCm39)	I212T	possibly damaging	Het
Pcnx4	T	C	12: 72,588,587 (GRCm39)	F132L	probably damaging	Het
Pde5a	T	A	3: 122,636,702 (GRCm39)	L717Q	probably damaging	Het
Peli2	A	T	14: 48,465,389 (GRCm39)		probably benign	Het
Phf14	A	G	6: 11,962,657 (GRCm39)	S435G	probably damaging	Het
Plekhg1	T	A	10: 3,913,564 (GRCm39)	H1095Q	probably damaging	Het
Plekhh2	A	G	17: 84,893,907 (GRCm39)		probably null	Het
Plekho1	T	G	3: 95,899,497 (GRCm39)	N99H	probably damaging	Het
Plxnc1	T	A	10: 94,742,395 (GRCm39)	K457N	probably benign	Het
Ppp1r3a	T	C	6: 14,718,322 (GRCm39)	E864G	probably benign	Het
Prkab2	T	A	3: 97,574,715 (GRCm39)	L237Q	probably damaging	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Ptger3	T	A	3: 157,273,207 (GRCm39)	C185S	probably damaging	Het
Ptprk	T	C	10: 28,230,709 (GRCm39)	Y267H	probably damaging	Het
Pum2	A	G	12: 8,794,654 (GRCm39)	I715V	probably benign	Het
R3hdm1	T	C	1: 128,114,573 (GRCm39)	V518A	probably damaging	Het
Rad54b	T	C	4: 11,606,272 (GRCm39)	L560P	probably damaging	Het
Rgs20	A	G	1: 5,140,370 (GRCm39)		probably null	Het
Sesn1	T	A	10: 41,781,315 (GRCm39)	L460H	probably damaging	Het
Slc39a14	A	G	14: 70,553,885 (GRCm39)		probably null	Het
Slco6c1	T	A	1: 96,990,201 (GRCm39)	H663L	probably benign	Het
Snx13	T	A	12: 35,132,926 (GRCm39)	C63S	probably benign	Het
Spmip4	T	A	6: 50,560,959 (GRCm39)	D212V	probably damaging	Het
Strip2	T	C	6: 29,941,940 (GRCm39)		probably null	Het
Syncrip	A	G	9: 88,361,620 (GRCm39)		probably benign	Het
Taf15	A	G	11: 83,395,579 (GRCm39)		probably benign	Het
Tbc1d8	T	C	1: 39,444,368 (GRCm39)		probably null	Het
Tgm4	T	A	9: 122,877,614 (GRCm39)	C205*	probably null	Het
Tmem212	A	T	3: 27,940,628 (GRCm39)	L63Q	possibly damaging	Het
Tmem63a	G	A	1: 180,790,054 (GRCm39)		probably null	Het
Trpm5	C	A	7: 142,636,298 (GRCm39)	V525L	probably benign	Het
Ttn	A	G	2: 76,537,171 (GRCm39)	L34919P	probably damaging	Het
Ttn	T	C	2: 76,694,619 (GRCm39)		probably benign	Het
Tuba4a	T	C	1: 75,194,069 (GRCm39)	I4V	possibly damaging	Het
Ubr4	A	G	4: 139,200,853 (GRCm39)	D4679G	possibly damaging	Het
Usp2	T	G	9: 44,003,445 (GRCm39)	V448G	probably damaging	Het
Usp3	A	G	9: 66,453,024 (GRCm39)		probably null	Het
Zfp341	T	A	2: 154,470,721 (GRCm39)	V246E	probably damaging	Het

Other mutations in Rab3d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02151:Rab3d	APN	9	21,827,020 (GRCm39)	missense	probably damaging	1.00
R0054:Rab3d	UTSW	9	21,827,222 (GRCm39)	missense	possibly damaging	0.82
R0616:Rab3d	UTSW	9	21,826,060 (GRCm39)	missense	probably damaging	1.00
R0629:Rab3d	UTSW	9	21,825,982 (GRCm39)	missense	probably benign	0.00
R3687:Rab3d	UTSW	9	21,826,204 (GRCm39)	missense	probably damaging	1.00
R6061:Rab3d	UTSW	9	21,821,815 (GRCm39)	missense	probably benign
R6062:Rab3d	UTSW	9	21,821,815 (GRCm39)	missense	probably benign
R6065:Rab3d	UTSW	9	21,821,815 (GRCm39)	missense	probably benign
R7962:Rab3d	UTSW	9	21,826,229 (GRCm39)	missense	probably damaging	1.00
R8966:Rab3d	UTSW	9	21,826,060 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCAGGGATAAAAGACGCCTCCC -3'
(R):5'- ACTCACCCTTACGGAAGCTG -3'

Sequencing Primer
(F):5'- GCCCCAAGCTGTTCTGTGTG -3'
(R):5'- TACGGAAGCTGCCCTCTTACAG -3'

Posted On

2014-11-12