Mutagenetix > Incidental Mutation

Incidental Mutation 'R0390:Kirrel3'

31610

Institutional Source

Beutler Lab

Gene Symbol

Kirrel3

Ensembl Gene

ENSMUSG00000032036

Gene Name

kirre like nephrin family adhesion molecule 3

Synonyms

2900036G11Rik, Neph2, 1500010O20Rik

MMRRC Submission

038596-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.203) question?

Stock #

R0390 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34485894-35036716 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 35020163 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 409 (I409N)

Ref Sequence

ENSEMBL: ENSMUSP00000139714 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000045091] [ENSMUST00000115148] [ENSMUST00000187182] [ENSMUST00000187625] [ENSMUST00000188658] [ENSMUST00000188933] [ENSMUST00000190549]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000045091
AA Change: I409N

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

SMART Domains

Protein: ENSMUSP00000048863
Gene: ENSMUSG00000032036
AA Change: I409N

Domain	Start	End	E-Value	Type
IG	21	111	1.35e-9	SMART
IG	122	214	2.56e-1	SMART
Pfam:Ig_2	217	298	2.1e-6	PFAM
IGc2	314	372	1.66e-9	SMART
IG	392	484	1.06e-2	SMART
transmembrane domain	491	513	N/A	INTRINSIC
low complexity region	568	581	N/A	INTRINSIC
low complexity region	700	717	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000115148
AA Change: I442N

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

SMART Domains

Protein: ENSMUSP00000110801
Gene: ENSMUSG00000032036
AA Change: I442N

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
IG	54	144	1.35e-9	SMART
IG	155	247	2.56e-1	SMART
Pfam:Ig_3	249	318	7.2e-6	PFAM
IGc2	347	405	1.66e-9	SMART
IG	425	517	1.06e-2	SMART
transmembrane domain	524	546	N/A	INTRINSIC
low complexity region	601	614	N/A	INTRINSIC
low complexity region	733	750	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000187182
AA Change: I416N

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

SMART Domains

Protein: ENSMUSP00000140219
Gene: ENSMUSG00000032036
AA Change: I416N

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
IG	28	118	1.35e-9	SMART
IG	129	221	2.56e-1	SMART
Pfam:Ig_2	224	305	2.3e-6	PFAM
IGc2	321	379	1.66e-9	SMART
IG	399	491	1.06e-2	SMART
transmembrane domain	510	532	N/A	INTRINSIC
low complexity region	612	625	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000187625
AA Change: I409N

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

SMART Domains

Protein: ENSMUSP00000139951
Gene: ENSMUSG00000032036
AA Change: I409N

Domain	Start	End	E-Value	Type
IG	21	111	1.35e-9	SMART
IG	122	214	2.56e-1	SMART
Pfam:Ig_2	217	298	2.1e-6	PFAM
IGc2	314	372	1.66e-9	SMART
IG	392	484	1.06e-2	SMART
transmembrane domain	491	513	N/A	INTRINSIC
low complexity region	568	581	N/A	INTRINSIC
low complexity region	700	717	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000188658
AA Change: I57N

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

SMART Domains

Protein: ENSMUSP00000140086
Gene: ENSMUSG00000032036
AA Change: I57N

Domain	Start	End	E-Value	Type
Pfam:Ig_2	1	31	1.4e-1	PFAM
IG	40	132	4.5e-5	SMART
transmembrane domain	151	173	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000188933
AA Change: I409N

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

SMART Domains

Protein: ENSMUSP00000139418
Gene: ENSMUSG00000032036
AA Change: I409N

Domain	Start	End	E-Value	Type
IG	21	111	5.7e-12	SMART
IG	122	214	1.1e-3	SMART
Pfam:Ig_2	217	298	3.7e-5	PFAM
IGc2	314	372	6.8e-12	SMART
IG	392	484	4.5e-5	SMART
transmembrane domain	503	525	N/A	INTRINSIC
low complexity region	580	593	N/A	INTRINSIC
low complexity region	712	729	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000190549
AA Change: I409N

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

SMART Domains

Protein: ENSMUSP00000139714
Gene: ENSMUSG00000032036
AA Change: I409N

Domain	Start	End	E-Value	Type
IG	21	111	5.7e-12	SMART
IG	122	214	1.1e-3	SMART
Pfam:Ig_2	217	298	2.6e-5	PFAM
IGc2	314	372	6.8e-12	SMART
IG	392	484	4.5e-5	SMART
transmembrane domain	491	513	N/A	INTRINSIC

Meta Mutation Damage Score

0.5774

Coding Region Coverage

1x: 99.1%
3x: 98.1%
10x: 95.9%
20x: 92.0%

Validation Efficiency

98% (110/112)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the nephrin-like protein family. These proteins are expressed in fetal and adult brain, and also in podocytes of kidney glomeruli. The cytoplasmic domains of these proteins interact with the C-terminus of podocin, also expressed in the podocytes, cells involved in ensuring size- and charge-selective ultrafiltration. Mutations in this gene are associated with mental retardation autosomal dominant type 4 (MRD4). Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired accessory olfactory bulb formation with reduced coalescence of vomeronasal sensory neuron axons in the posterior accessory olfactory bulb, loss of male-male aggression and abnormal male sexual response to a male intruder mouse. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 110 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A730017C20Rik	T	A	18: 59,075,688 (GRCm38)	V136E	probably damaging	Het
Adam18	C	T	8: 24,674,054 (GRCm38)	G38R	probably benign	Het
Ap2m1	T	C	16: 20,541,099 (GRCm38)	M183T	probably damaging	Het
Apob	A	T	12: 7,988,678 (GRCm38)	I364F	probably damaging	Het
Arl6	A	T	16: 59,622,421 (GRCm38)		probably benign	Het
Cand2	A	G	6: 115,774,653 (GRCm38)	M15V	possibly damaging	Het
Cbl	A	G	9: 44,201,005 (GRCm38)	F131S	probably damaging	Het
Ccdc151	T	A	9: 21,991,708 (GRCm38)	H442L	probably benign	Het
Ccdc74a	A	G	16: 17,650,476 (GRCm38)	S321G	probably benign	Het
Cdc14b	T	C	13: 64,210,192 (GRCm38)		probably benign	Het
Cep152	T	C	2: 125,576,869 (GRCm38)		probably benign	Het
Cep290	A	G	10: 100,508,758 (GRCm38)	E479G	probably benign	Het
Chrm2	T	G	6: 36,524,111 (GRCm38)	I301R	probably benign	Het
Clec2e	A	G	6: 129,093,468 (GRCm38)	W197R	probably damaging	Het
Cnot10	G	T	9: 114,629,150 (GRCm38)	S96*	probably null	Het
Col19a1	A	G	1: 24,289,655 (GRCm38)		probably benign	Het
Csmd2	T	C	4: 128,133,673 (GRCm38)		probably benign	Het
Cthrc1	A	T	15: 39,086,764 (GRCm38)	*172L	probably null	Het
Cul9	A	T	17: 46,528,589 (GRCm38)	I821N	probably benign	Het
Daam1	G	C	12: 71,975,304 (GRCm38)		probably benign	Het
Dhx58	A	T	11: 100,699,264 (GRCm38)	I398N	probably damaging	Het
Dip2b	T	A	15: 100,193,913 (GRCm38)	H844Q	probably damaging	Het
Dmac2	A	G	7: 25,621,029 (GRCm38)	D50G	probably damaging	Het
Dmxl1	C	A	18: 49,879,362 (GRCm38)	Q1529K	probably benign	Het
Dtna	C	T	18: 23,597,501 (GRCm38)	P315L	probably damaging	Het
Ep300	T	C	15: 81,640,116 (GRCm38)	S1382P	unknown	Het
Fat2	A	T	11: 55,310,777 (GRCm38)	N490K	probably damaging	Het
Flg2	T	A	3: 93,200,355 (GRCm38)		probably benign	Het
Gm13084	T	A	4: 143,811,699 (GRCm38)	D234V	probably benign	Het
Gpatch1	T	C	7: 35,281,381 (GRCm38)		probably benign	Het
Grin2a	C	A	16: 9,579,585 (GRCm38)	K879N	possibly damaging	Het
Hacd3	A	C	9: 65,001,022 (GRCm38)	I164S	possibly damaging	Het
Hinfp	A	C	9: 44,298,948 (GRCm38)	C197G	probably damaging	Het
Hsd17b12	T	C	2: 94,114,990 (GRCm38)		probably benign	Het
Hsd3b1	A	T	3: 98,853,039 (GRCm38)	L212Q	probably damaging	Het
Ifrd1	C	T	12: 40,214,094 (GRCm38)		probably null	Het
Igf2bp2	A	G	16: 22,081,801 (GRCm38)	F129L	possibly damaging	Het
Klhdc10	T	C	6: 30,447,412 (GRCm38)	I204T	probably damaging	Het
Kpna6	A	T	4: 129,657,804 (GRCm38)	S65R	possibly damaging	Het
Lama3	A	T	18: 12,407,563 (GRCm38)	D308V	probably benign	Het
Larp4b	T	A	13: 9,158,107 (GRCm38)		probably null	Het
Lgr6	C	T	1: 134,994,010 (GRCm38)	A199T	probably damaging	Het
Lyzl1	A	T	18: 4,169,175 (GRCm38)	T11S	probably benign	Het
Man1c1	A	G	4: 134,578,315 (GRCm38)	L366P	probably damaging	Het
Mef2a	A	G	7: 67,251,724 (GRCm38)	M100T	probably damaging	Het
Mettl13	G	A	1: 162,538,889 (GRCm38)	H474Y	possibly damaging	Het
Mmp3	A	G	9: 7,451,320 (GRCm38)	D352G	probably benign	Het
Mns1	T	C	9: 72,452,804 (GRCm38)	I412T	probably damaging	Het
Mon2	T	C	10: 123,007,021 (GRCm38)	D1501G	probably null	Het
Mylk	G	T	16: 34,875,620 (GRCm38)	G242W	probably damaging	Het
Nav1	T	C	1: 135,449,966 (GRCm38)	D1715G	possibly damaging	Het
Nckap1l	T	C	15: 103,453,883 (GRCm38)	S2P	probably damaging	Het
Nek3	A	T	8: 22,128,729 (GRCm38)		probably benign	Het
Nfrkb	A	G	9: 31,388,897 (GRCm38)		probably benign	Het
Nlrp4d	T	C	7: 10,388,778 (GRCm38)	D53G	probably benign	Het
Nol8	T	C	13: 49,662,152 (GRCm38)	S561P	probably damaging	Het
Nuf2	A	C	1: 169,525,297 (GRCm38)		probably benign	Het
Ofcc1	T	A	13: 40,015,313 (GRCm38)	D866V	possibly damaging	Het
Olfr195	A	G	16: 59,149,299 (GRCm38)	I150V	probably benign	Het
Optn	A	G	2: 5,046,195 (GRCm38)	L125P	probably benign	Het
Otoa	T	A	7: 121,131,341 (GRCm38)	F588Y	probably benign	Het
Pappa	T	A	4: 65,351,613 (GRCm38)		probably null	Het
Pde5a	T	G	3: 122,835,583 (GRCm38)	C635W	probably damaging	Het
Pdgfb	A	T	15: 80,003,419 (GRCm38)		probably null	Het
Pih1d2	T	A	9: 50,621,046 (GRCm38)	C135S	probably damaging	Het
Plcg1	G	T	2: 160,752,366 (GRCm38)	C361F	probably damaging	Het
Ppp4r4	T	C	12: 103,601,360 (GRCm38)		probably benign	Het
Prdm10	G	A	9: 31,349,268 (GRCm38)		probably null	Het
Prex2	T	A	1: 11,089,706 (GRCm38)		probably null	Het
Prss56	T	G	1: 87,184,730 (GRCm38)		probably null	Het
Prtg	A	G	9: 72,844,958 (GRCm38)	K209E	probably benign	Het
Ptprc	G	A	1: 138,122,575 (GRCm38)	T36I	possibly damaging	Het
Rasgrp4	A	G	7: 29,145,860 (GRCm38)	Y302C	probably damaging	Het
Rb1cc1	T	A	1: 6,248,634 (GRCm38)	M759K	probably damaging	Het
Rbm15b	T	A	9: 106,885,998 (GRCm38)	M324L	probably benign	Het
Rcbtb2	T	C	14: 73,178,547 (GRCm38)	V500A	probably damaging	Het
Rgs6	A	G	12: 83,133,677 (GRCm38)	K434R	probably damaging	Het
Rims1	C	T	1: 22,596,526 (GRCm38)	A125T	possibly damaging	Het
Robo3	A	G	9: 37,422,177 (GRCm38)	V746A	probably benign	Het
Rtl1	C	T	12: 109,591,386 (GRCm38)	E1340K	unknown	Het
Sacs	G	A	14: 61,205,640 (GRCm38)	D1712N	possibly damaging	Het
Samd4b	G	A	7: 28,403,977 (GRCm38)	P19S	probably benign	Het
Samhd1	T	C	2: 157,114,231 (GRCm38)	Y347C	probably damaging	Het
Sema6d	T	A	2: 124,658,490 (GRCm38)	I393N	probably damaging	Het
Sigmar1	C	T	4: 41,741,243 (GRCm38)	A4T	probably benign	Het
Skint9	C	A	4: 112,389,179 (GRCm38)	L245F	probably benign	Het
Slc35f5	T	C	1: 125,585,095 (GRCm38)	L372P	probably damaging	Het
Smc1b	A	T	15: 85,066,277 (GRCm38)	I1182N	probably damaging	Het
Smyd3	A	G	1: 178,957,573 (GRCm38)		probably benign	Het
Sptlc1	T	C	13: 53,337,612 (GRCm38)	D417G	probably benign	Het
Sv2c	T	C	13: 96,088,708 (GRCm38)	N31S	probably benign	Het
Tjp1	T	C	7: 65,314,990 (GRCm38)	D811G	probably damaging	Het
Top2b	A	G	14: 16,418,442 (GRCm38)	T1221A	probably benign	Het
Tph2	T	C	10: 115,174,109 (GRCm38)	D182G	probably damaging	Het
Traf6	C	T	2: 101,688,588 (GRCm38)	Q141*	probably null	Het
Ttn	T	C	2: 76,756,931 (GRCm38)	D21574G	probably damaging	Het
Uba2	T	A	7: 34,151,021 (GRCm38)	N367I	probably benign	Het
Ube2b	T	C	11: 51,988,602 (GRCm38)		probably benign	Het
Ubr5	G	T	15: 38,030,672 (GRCm38)	L426I	probably benign	Het
Ugt2a2	T	A	5: 87,464,148 (GRCm38)	H301L	probably benign	Het
Upf2	T	A	2: 6,018,894 (GRCm38)		probably benign	Het
Utrn	T	C	10: 12,710,060 (GRCm38)	D991G	probably benign	Het
Vmn2r25	T	C	6: 123,823,181 (GRCm38)	D734G	probably damaging	Het
Vmn2r68	T	A	7: 85,233,249 (GRCm38)		probably benign	Het
Vmn2r68	C	G	7: 85,233,258 (GRCm38)		probably null	Het
Vwf	T	A	6: 125,626,361 (GRCm38)	Y891*	probably null	Het
Wwox	C	T	8: 114,706,278 (GRCm38)	T228I	probably benign	Het
Zer1	C	T	2: 30,108,213 (GRCm38)		probably benign	Het
Zfp180	C	T	7: 24,104,707 (GRCm38)	H184Y	possibly damaging	Het
Zfp68	A	T	5: 138,607,225 (GRCm38)	Y279N	probably benign	Het

Other mutations in Kirrel3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00919:Kirrel3	APN	9	35,015,253 (GRCm38)	critical splice acceptor site	probably null
IGL01369:Kirrel3	APN	9	35,016,441 (GRCm38)	missense	probably benign	0.07
IGL01837:Kirrel3	APN	9	35,034,928 (GRCm38)	missense	probably damaging	1.00
IGL01950:Kirrel3	APN	9	35,028,329 (GRCm38)	splice site	probably benign
IGL01973:Kirrel3	APN	9	35,016,468 (GRCm38)	missense	probably damaging	1.00
IGL01994:Kirrel3	APN	9	35,020,133 (GRCm38)	missense	possibly damaging	0.71
IGL03184:Kirrel3	APN	9	35,007,756 (GRCm38)	missense	probably damaging	1.00
R0033:Kirrel3	UTSW	9	35,000,963 (GRCm38)	missense	probably benign	0.06
R0033:Kirrel3	UTSW	9	35,000,963 (GRCm38)	missense	probably benign	0.06
R0038:Kirrel3	UTSW	9	34,911,770 (GRCm38)	splice site	probably null
R0038:Kirrel3	UTSW	9	34,911,770 (GRCm38)	splice site	probably null
R0627:Kirrel3	UTSW	9	35,035,174 (GRCm38)	missense	probably damaging	1.00
R0786:Kirrel3	UTSW	9	35,034,865 (GRCm38)	missense	probably damaging	1.00
R0920:Kirrel3	UTSW	9	35,028,352 (GRCm38)	missense	probably damaging	1.00
R0962:Kirrel3	UTSW	9	35,000,997 (GRCm38)	missense	possibly damaging	0.95
R1716:Kirrel3	UTSW	9	35,023,547 (GRCm38)	missense	probably damaging	1.00
R2010:Kirrel3	UTSW	9	34,939,198 (GRCm38)	missense	probably damaging	1.00
R4289:Kirrel3	UTSW	9	35,023,473 (GRCm38)	missense	probably benign	0.44
R4888:Kirrel3	UTSW	9	35,013,305 (GRCm38)	missense	probably damaging	1.00
R4970:Kirrel3	UTSW	9	34,944,439 (GRCm38)	missense	possibly damaging	0.88
R5121:Kirrel3	UTSW	9	35,013,305 (GRCm38)	missense	probably damaging	1.00
R5368:Kirrel3	UTSW	9	35,007,738 (GRCm38)	missense	probably damaging	1.00
R5572:Kirrel3	UTSW	9	35,000,948 (GRCm38)	missense	probably damaging	1.00
R5707:Kirrel3	UTSW	9	35,013,276 (GRCm38)	missense	probably damaging	1.00
R6302:Kirrel3	UTSW	9	35,007,749 (GRCm38)	missense	probably damaging	1.00
R6449:Kirrel3	UTSW	9	34,990,973 (GRCm38)	missense	probably benign
R6908:Kirrel3	UTSW	9	35,013,401 (GRCm38)	missense	possibly damaging	0.86
R6967:Kirrel3	UTSW	9	35,034,906 (GRCm38)	missense	probably damaging	1.00
R7578:Kirrel3	UTSW	9	34,939,112 (GRCm38)	missense	probably damaging	1.00
R7861:Kirrel3	UTSW	9	35,020,123 (GRCm38)	missense	possibly damaging	0.79
R8094:Kirrel3	UTSW	9	35,035,164 (GRCm38)	missense	probably damaging	1.00
R8383:Kirrel3	UTSW	9	35,029,883 (GRCm38)	missense	probably null	0.89
R8494:Kirrel3	UTSW	9	34,991,045 (GRCm38)	missense	probably benign	0.03
R8878:Kirrel3	UTSW	9	34,939,265 (GRCm38)	splice site	probably benign
R8955:Kirrel3	UTSW	9	34,944,442 (GRCm38)	missense	probably damaging	1.00
R9140:Kirrel3	UTSW	9	35,013,300 (GRCm38)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- GGATTGGTGGACACGCTTCTGAAC -3'
(R):5'- ATGGAAGGCACAGAGTACCTCCTG -3'

Sequencing Primer
(F):5'- ACCCATCAAAAGAGGGTGC -3'
(R):5'- GGTGCCTAATTCAGTCTGAATCAC -3'

Posted On

2013-04-24