Mutagenetix > Incidental Mutation

Incidental Mutation 'R4940:Rnf13'

382980

Institutional Source

Beutler Lab

Gene Symbol

Rnf13

Ensembl Gene

ENSMUSG00000036503

Gene Name

ring finger protein 13

Synonyms

2010001H16Rik, Rzf

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4940 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

57736062-57835233 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 57796206 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 110 (N110K)

Ref Sequence

ENSEMBL: ENSMUSP00000143692 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041826] [ENSMUST00000197205] [ENSMUST00000198214] [ENSMUST00000198249] [ENSMUST00000199041] [ENSMUST00000200497]

AlphaFold

O54965

Predicted Effect

probably benign
Transcript: ENSMUST00000041826
AA Change: N110K

PolyPhen 2 Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000049331
Gene: ENSMUSG00000036503
AA Change: N110K

Domain	Start	End	E-Value	Type
Pfam:PA	63	160	1.3e-14	PFAM
transmembrane domain	182	204	N/A	INTRINSIC
low complexity region	208	226	N/A	INTRINSIC
RING	240	281	1.85e-8	SMART
low complexity region	291	299	N/A	INTRINSIC
low complexity region	336	357	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000197205
AA Change: N110K

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000143692
Gene: ENSMUSG00000036503
AA Change: N110K

Domain	Start	End	E-Value	Type
signal peptide	1	34	N/A	INTRINSIC
Pfam:PA	62	153	2.9e-9	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197783

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197920

Predicted Effect

possibly damaging
Transcript: ENSMUST00000198214
AA Change: N110K

PolyPhen 2 Score 0.498 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000143498
Gene: ENSMUSG00000036503
AA Change: N110K

Domain	Start	End	E-Value	Type
Pfam:PA	63	160	5.1e-15	PFAM
transmembrane domain	182	204	N/A	INTRINSIC
low complexity region	208	226	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000198249
AA Change: N83K

PolyPhen 2 Score 0.575 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000142828
Gene: ENSMUSG00000036503
AA Change: N83K

Domain	Start	End	E-Value	Type
Pfam:PA	33	131	2.5e-12	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000198996

Predicted Effect

probably benign
Transcript: ENSMUST00000199041
AA Change: N110K

PolyPhen 2 Score 0.392 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000142335
Gene: ENSMUSG00000036503
AA Change: N110K

Domain	Start	End	E-Value	Type
Pfam:PA	59	162	6.6e-15	PFAM
transmembrane domain	182	204	N/A	INTRINSIC
SCOP:d1ldjb_	211	260	2e-7	SMART
Blast:RING	240	267	5e-9	BLAST

Predicted Effect

possibly damaging
Transcript: ENSMUST00000200497
AA Change: N110K

PolyPhen 2 Score 0.503 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000142462
Gene: ENSMUSG00000036503
AA Change: N110K

Domain	Start	End	E-Value	Type
Pfam:PA	59	162	1.1e-14	PFAM
transmembrane domain	182	204	N/A	INTRINSIC
SCOP:d1ldjb_	211	260	1e-7	SMART
Blast:RING	240	261	9e-8	BLAST
low complexity region	262	270	N/A	INTRINSIC
low complexity region	307	328	N/A	INTRINSIC

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.5%
20x: 93.3%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a member of the PA-TM-RING family of proteins that contain a protease associated (PA) domain and a RING finger domain separated by a transmembrane (TM) domain. The encoded protein is an E3 ubiquitin ligase localized to the endosomal-lysosomal vesicles and inner nuclear membrane. Mice lacking the encoded protein have impaired learning abilities associated with a decreased synaptic vesicle density and dysregulated SNARE complex assembly. Alternative splicing of this gene results in multiple transcript variants. A pseudogene for this gene has been identified on the X chromosome. [provided by RefSeq, Jan 2015]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700007G11Rik	A	G	5: 98,737,636	H134R	possibly damaging	Het
3632451O06Rik	A	T	14: 49,773,482	M256K	probably benign	Het
4931414P19Rik	T	C	14: 54,591,325	T240A	probably benign	Het
Abca15	T	C	7: 120,332,694	Y57H	probably benign	Het
Adgrf4	A	G	17: 42,666,529	I641T	possibly damaging	Het
Ankrd11	A	G	8: 122,889,821	Y2410H	probably damaging	Het
Apbb2	C	A	5: 66,452,261	L14F	probably null	Het
Arhgdia	T	C	11: 120,579,235	D204G	probably damaging	Het
Catsperd	A	T	17: 56,662,736	Y610F	possibly damaging	Het
Cblb	T	A	16: 52,033,103	D27E	probably damaging	Het
Ccdc180	A	T	4: 45,917,453	I893F	probably damaging	Het
Ccdc180	A	G	4: 45,917,508	H911R	probably damaging	Het
Cdh23	T	A	10: 60,307,935	I2966F	probably damaging	Het
Chat	G	A	14: 32,419,105	P445L	probably damaging	Het
Chdh	G	T	14: 30,032,852	R273L	possibly damaging	Het
Clic3	T	C	2: 25,457,917	V72A	probably benign	Het
Cyp2d12	T	A	15: 82,558,050	D244E	probably benign	Het
Ddr1	T	A	17: 35,690,130	D241V	probably damaging	Het
Dock7	T	A	4: 99,020,077	K605N	probably damaging	Het
Dsg2	T	A	18: 20,579,430	F164I	probably damaging	Het
Dstyk	T	A	1: 132,453,106	N446K	probably damaging	Het
Epb42	A	T	2: 121,034,451	L53Q	probably damaging	Het
Extl2	G	C	3: 116,027,192	K229N	probably benign	Het
Frmd4b	T	A	6: 97,298,090	S617C	probably damaging	Het
Fscb	C	T	12: 64,473,814	V293I	probably benign	Het
Glp2r	G	T	11: 67,757,593	Y94*	probably null	Het
Gm4978	A	C	9: 69,450,872		probably benign	Het
Gm6729	A	G	10: 86,540,388		noncoding transcript	Het
Gnat2	A	C	3: 108,100,616	N293T	probably benign	Het
Herpud1	T	C	8: 94,390,842	I142T	probably benign	Het
Irak2	G	A	6: 113,693,730	V536I	probably benign	Het
Kcnu1	A	T	8: 25,897,862		probably null	Het
Kdm4a	A	G	4: 118,161,754	S422P	probably benign	Het
Lair1	T	A	7: 4,028,949	D53V	probably benign	Het
Lhx1	G	T	11: 84,519,909	Y196*	probably null	Het
Lrrc37a	G	A	11: 103,497,612	T2329I	unknown	Het
Mag	T	C	7: 30,909,200	D163G	probably damaging	Het
Magi3	A	G	3: 104,051,392	V459A	probably damaging	Het
Med13	A	G	11: 86,288,118	Y1451H	probably damaging	Het
Megf8	T	A	7: 25,360,706	C2341S	probably damaging	Het
Mppe1	A	G	18: 67,228,024	C221R	probably damaging	Het
Mtus1	T	A	8: 41,041,478	H39L	possibly damaging	Het
Nkpd1	C	T	7: 19,523,573	Q276*	probably null	Het
Nkx3-1	G	A	14: 69,190,918	G72S	probably benign	Het
Nutm2	T	C	13: 50,474,873	C658R	possibly damaging	Het
Olfm1	T	C	2: 28,222,590	V239A	possibly damaging	Het
Pcnx	C	T	12: 81,917,793	H245Y	possibly damaging	Het
Pgm3	A	G	9: 86,559,476	L356S	probably damaging	Het
Pik3r4	C	G	9: 105,668,994	H207D	probably benign	Het
Pkd1l1	T	C	11: 8,844,585	T1859A	probably benign	Het
Pon3	A	T	6: 5,221,625	V335E	possibly damaging	Het
Ppp4r3b	A	G	11: 29,211,740	T705A	probably benign	Het
Prmt7	T	C	8: 106,237,278	V268A	probably benign	Het
Psd	C	T	19: 46,322,417	G398R	probably damaging	Het
Pygl	A	G	12: 70,206,381	V188A	probably damaging	Het
Rnf170	C	T	8: 26,125,911	Q77*	probably null	Het
Rrp8	A	T	7: 105,734,077	Y327*	probably null	Het
Ruvbl2	T	C	7: 45,424,726	D228G	probably damaging	Het
Scgn	T	A	13: 23,989,824	T35S	probably benign	Het
Scyl3	C	T	1: 163,934,747	P74S	probably damaging	Het
Sec61b	T	G	4: 47,483,074	S123A	probably benign	Het
Sertad2	T	C	11: 20,647,899	S32P	possibly damaging	Het
Slc23a3	T	C	1: 75,133,803		probably null	Het
Sult2a2	T	G	7: 13,738,298	V140G	probably benign	Het
Tbc1d4	A	T	14: 101,507,231	S320T	probably benign	Het
Trabd2b	T	C	4: 114,408,944	Y52H	probably damaging	Het
Traf2	T	C	2: 25,530,288	E183G	probably null	Het
Trip10	G	T	17: 57,263,017	V561F	possibly damaging	Het
Ttc7	G	T	17: 87,306,958	V184F	probably benign	Het
Ubc	A	G	5: 125,386,229	V678A	probably benign	Het
Unk	A	G	11: 116,053,665	E414G	possibly damaging	Het
Usp42	T	C	5: 143,719,762	N365D	probably damaging	Het
Zbtb26	A	T	2: 37,436,769	I85K	probably damaging	Het
Zfhx2	A	T	14: 55,066,434	H1364Q	possibly damaging	Het

Other mutations in Rnf13

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01367:Rnf13	APN	3	57807087	missense	probably benign	0.06
IGL01835:Rnf13	APN	3	57820586	missense	probably damaging	1.00
IGL02219:Rnf13	APN	3	57796223	missense	probably damaging	1.00
IGL02675:Rnf13	APN	3	57779396	missense	probably benign	0.17
IGL03015:Rnf13	APN	3	57833744	missense	possibly damaging	0.74
IGL03246:Rnf13	APN	3	57769050	missense	probably damaging	0.98
solomon	UTSW	3	57820534	nonsense	probably null
BB005:Rnf13	UTSW	3	57764308	missense	probably benign	0.18
BB015:Rnf13	UTSW	3	57764308	missense	probably benign	0.18
R0147:Rnf13	UTSW	3	57802468	missense	probably damaging	0.98
R0481:Rnf13	UTSW	3	57779451	missense	probably damaging	1.00
R0481:Rnf13	UTSW	3	57807053	missense	probably damaging	1.00
R1389:Rnf13	UTSW	3	57779496	missense	probably damaging	1.00
R2146:Rnf13	UTSW	3	57802486	missense	probably null	0.99
R3964:Rnf13	UTSW	3	57769112	missense	probably damaging	0.96
R4444:Rnf13	UTSW	3	57820589	missense	probably damaging	1.00
R4446:Rnf13	UTSW	3	57820589	missense	probably damaging	1.00
R4489:Rnf13	UTSW	3	57820589	missense	probably damaging	1.00
R4810:Rnf13	UTSW	3	57796272	missense	probably damaging	0.99
R6233:Rnf13	UTSW	3	57832970	missense	possibly damaging	0.83
R7002:Rnf13	UTSW	3	57833612	missense	probably damaging	0.96
R7622:Rnf13	UTSW	3	57820534	nonsense	probably null
R7652:Rnf13	UTSW	3	57764351	missense	probably benign	0.01
R7928:Rnf13	UTSW	3	57764308	missense	probably benign	0.18
R8011:Rnf13	UTSW	3	57807070	nonsense	probably null
R8893:Rnf13	UTSW	3	57807099	missense	probably damaging	0.97
R9086:Rnf13	UTSW	3	57833576	missense	probably benign	0.16
R9116:Rnf13	UTSW	3	57802445	critical splice acceptor site	probably null
R9479:Rnf13	UTSW	3	57820562	missense	possibly damaging	0.85
R9616:Rnf13	UTSW	3	57833009	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- AGAAAGCATCTAAAGACCTCCTAGG -3'
(R):5'- TAGGAATTAAGAGTACCCCAAGACC -3'

Sequencing Primer
(F):5'- AGGTGTTCTCCTATAGGCATCTAC -3'
(R):5'- ACTATCTGATACTGAAGAGACATCAC -3'

Posted On

2016-04-27