Mutagenetix > Incidental Mutation

Incidental Mutation 'R0092:Necab3'

20260

Institutional Source

Beutler Lab

Gene Symbol

Necab3

Ensembl Gene

ENSMUSG00000027489

Gene Name

N-terminal EF-hand calcium binding protein 3

Synonyms

Apba2bp, XB51, 2900010M17Rik, Nip1

MMRRC Submission

038379-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.133) question?

Stock #

R0092 (G1)

Quality Score

101

Status

Validated (trace)

Chromosome

Chromosomal Location

154386319-154400810 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 154400659 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 34 (D34G)

Ref Sequence

ENSEMBL: ENSMUSP00000105338 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000894] [ENSMUST00000000895] [ENSMUST00000103145] [ENSMUST00000109716] [ENSMUST00000125793]

AlphaFold

Q9D6J4

Predicted Effect

probably benign
Transcript: ENSMUST00000000894

SMART Domains

Protein: ENSMUSP00000000894
Gene: ENSMUSG00000027490

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Pfam:E2F_TDP	77	142	1.1e-25	PFAM
low complexity region	156	173	N/A	INTRINSIC
low complexity region	273	295	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000000895
AA Change: D34G

PolyPhen 2 Score 0.889 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000000895
Gene: ENSMUSG00000027489
AA Change: D34G

Domain	Start	End	E-Value	Type
Pfam:EF-hand_1	31	58	7.3e-8	PFAM
Pfam:EF-hand_5	32	57	4.6e-9	PFAM
low complexity region	180	203	N/A	INTRINSIC
coiled coil region	209	237	N/A	INTRINSIC
Pfam:ABM	252	327	4.4e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000103145

SMART Domains

Protein: ENSMUSP00000099434
Gene: ENSMUSG00000027490

Domain	Start	End	E-Value	Type
low complexity region	11	26	N/A	INTRINSIC
low complexity region	62	82	N/A	INTRINSIC
E2F_TDP	122	187	1.63e-30	SMART
Pfam:E2F_CC-MB	201	294	2.2e-37	PFAM
low complexity region	318	340	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000109716
AA Change: D34G

PolyPhen 2 Score 0.889 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000105338
Gene: ENSMUSG00000027489
AA Change: D34G

Domain	Start	End	E-Value	Type
Pfam:EF-hand_1	31	59	6.9e-8	PFAM
Pfam:EF-hand_5	32	57	1.7e-9	PFAM
low complexity region	180	203	N/A	INTRINSIC
Pfam:ABM	232	303	2.7e-10	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124382

Predicted Effect

possibly damaging
Transcript: ENSMUST00000125793
AA Change: D34G

PolyPhen 2 Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000117090
Gene: ENSMUSG00000027489
AA Change: D34G

Domain	Start	End	E-Value	Type
low complexity region	146	168	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135530

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149725

Meta Mutation Damage Score

0.3466

Coding Region Coverage

1x: 98.9%
3x: 97.9%
10x: 95.1%
20x: 88.6%

Validation Efficiency

99% (112/113)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene interacts with the amino-terminal domain of the neuron-specific X11-like protein (X11L), inhibits the association of X11L with amyloid precursor protein through a non-competitive mechanism, and abolishes the suppression of beta-amyloid production by X11L. This protein, together with X11L, may play an important role in the regulatory system of amyloid precursor protein metabolism and beta-amyloid generation. The protein is phosphorylated by NIMA-related expressed kinase 2, and localizes to the Golgi apparatus. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcg2	T	A	6: 58,662,762 (GRCm39)	S535T	probably benign	Het
Acad11	A	T	9: 103,967,540 (GRCm39)		probably benign	Het
Acadm	A	T	3: 153,647,512 (GRCm39)		probably benign	Het
Acot12	T	A	13: 91,889,684 (GRCm39)	M12K	probably damaging	Het
Actr2	A	T	11: 20,044,308 (GRCm39)	N99K	probably benign	Het
Adam2	G	A	14: 66,291,336 (GRCm39)	A314V	probably damaging	Het
Agl	C	T	3: 116,587,453 (GRCm39)	R34Q	probably damaging	Het
Agrn	C	T	4: 156,263,410 (GRCm39)	R338H	probably damaging	Het
AI661453	A	G	17: 47,778,440 (GRCm39)		probably benign	Het
Alpk3	A	G	7: 80,742,301 (GRCm39)	D706G	probably benign	Het
Apbb1	T	C	7: 105,208,361 (GRCm39)	E648G	probably damaging	Het
Astn2	C	A	4: 66,322,219 (GRCm39)	A127S	unknown	Het
Asxl2	T	C	12: 3,546,313 (GRCm39)	S366P	probably benign	Het
Bdh1	A	T	16: 31,266,380 (GRCm39)	K92*	probably null	Het
Bltp1	A	G	3: 37,082,308 (GRCm39)	D3790G	probably benign	Het
Cacna1g	C	T	11: 94,348,090 (GRCm39)	S666N	probably damaging	Het
Ces2b	A	G	8: 105,563,144 (GRCm39)	T361A	possibly damaging	Het
Col6a4	T	A	9: 105,890,513 (GRCm39)	E1927V	probably benign	Het
Ctnnb1	T	G	9: 120,781,929 (GRCm39)	I314S	possibly damaging	Het
Cyp2c66	T	C	19: 39,172,224 (GRCm39)		probably benign	Het
Dennd4c	T	A	4: 86,699,844 (GRCm39)	F232I	probably damaging	Het
Dennd5a	T	C	7: 109,499,013 (GRCm39)	N950S	possibly damaging	Het
Dhx30	T	C	9: 109,914,078 (GRCm39)	N14S	possibly damaging	Het
Dip2b	T	A	15: 100,100,146 (GRCm39)	V1004D	probably damaging	Het
Dnah1	A	C	14: 30,993,566 (GRCm39)	S2872A	probably benign	Het
Dnajc10	T	C	2: 80,156,026 (GRCm39)	V233A	probably damaging	Het
E230025N22Rik	A	G	18: 36,822,277 (GRCm39)	L162P	probably damaging	Het
Elmod3	T	C	6: 72,543,792 (GRCm39)	D333G	probably benign	Het
Epb41l3	T	A	17: 69,593,745 (GRCm39)	M846K	probably damaging	Het
Frem2	A	G	3: 53,497,217 (GRCm39)	Y1766H	probably benign	Het
Fxr2	T	C	11: 69,532,972 (GRCm39)		probably benign	Het
Gmpr2	A	G	14: 55,915,402 (GRCm39)	R258G	probably benign	Het
Helb	T	C	10: 119,925,713 (GRCm39)	Y888C	probably damaging	Het
Hephl1	TTCCAGATGTCC	TTCC	9: 15,001,899 (GRCm39)		probably null	Het
Hipk2	T	C	6: 38,720,164 (GRCm39)	D482G	probably damaging	Het
Itgb4	G	T	11: 115,869,950 (GRCm39)	R44L	probably damaging	Het
Itih1	T	C	14: 30,662,820 (GRCm39)		probably benign	Het
Kit	T	A	5: 75,808,414 (GRCm39)	S719R	possibly damaging	Het
Krt13	G	A	11: 100,012,258 (GRCm39)	Q22*	probably null	Het
L3mbtl4	A	C	17: 68,732,698 (GRCm39)	R59S	probably benign	Het
Lpp	A	G	16: 24,580,352 (GRCm39)	S23G	probably benign	Het
Magi3	G	A	3: 103,958,280 (GRCm39)	Q602*	probably null	Het
Man2a1	A	G	17: 64,966,079 (GRCm39)		probably benign	Het
Muc5ac	A	G	7: 141,372,367 (GRCm39)	E2667G	possibly damaging	Het
Myef2l	G	A	3: 10,153,633 (GRCm39)	C134Y	possibly damaging	Het
Myo15b	C	G	11: 115,753,812 (GRCm39)	S842C	possibly damaging	Het
Naf1	T	A	8: 67,341,760 (GRCm39)	S462T	probably benign	Het
Nisch	C	A	14: 30,913,410 (GRCm39)		probably benign	Het
Nlrc5	T	C	8: 95,216,222 (GRCm39)		probably benign	Het
Nmt1	T	C	11: 102,937,319 (GRCm39)	F119L	probably damaging	Het
Nod1	T	G	6: 54,921,526 (GRCm39)	D264A	probably damaging	Het
Nol8	C	T	13: 49,815,923 (GRCm39)	A677V	possibly damaging	Het
Nt5e	T	A	9: 88,252,338 (GRCm39)	F567I	probably benign	Het
Obscn	A	T	11: 58,942,073 (GRCm39)	M4434K	possibly damaging	Het
Opa1	A	T	16: 29,444,412 (GRCm39)	D866V	probably damaging	Het
Or10a3m	T	C	7: 108,313,031 (GRCm39)	V145A	probably benign	Het
Or10al3	T	G	17: 38,011,696 (GRCm39)	L45R	probably damaging	Het
Or10p1	A	G	10: 129,444,090 (GRCm39)	S87P	probably damaging	Het
Or1j21	A	G	2: 36,683,508 (GRCm39)	T87A	probably benign	Het
Or51ai2	T	C	7: 103,586,934 (GRCm39)	S116P	probably damaging	Het
Otop1	T	A	5: 38,457,174 (GRCm39)	V311E	probably damaging	Het
Pcsk2	A	G	2: 143,642,944 (GRCm39)	D407G	probably damaging	Het
Pdcd1	A	G	1: 93,980,149 (GRCm39)	W23R	possibly damaging	Het
Pigp	A	G	16: 94,166,321 (GRCm39)	V129A	probably damaging	Het
Pik3r5	A	G	11: 68,383,629 (GRCm39)	R483G	probably benign	Het
Pink1	A	G	4: 138,047,309 (GRCm39)	V225A	probably benign	Het
Plcl1	C	G	1: 55,735,924 (GRCm39)	Q422E	probably damaging	Het
Plec	T	C	15: 76,067,943 (GRCm39)	E1222G	probably benign	Het
Polr1a	T	C	6: 71,944,439 (GRCm39)		probably benign	Het
Prokr2	C	T	2: 132,215,517 (GRCm39)	V154M	probably damaging	Het
Rasgrp4	A	G	7: 28,844,557 (GRCm39)	R280G	possibly damaging	Het
Rmnd5b	T	C	11: 51,520,419 (GRCm39)	E8G	possibly damaging	Het
Sbf2	T	A	7: 109,920,013 (GRCm39)		probably benign	Het
Sec23b	A	G	2: 144,408,830 (GRCm39)	M172V	probably benign	Het
Setx	T	C	2: 29,036,305 (GRCm39)	V930A	probably benign	Het
Sft2d2	G	A	1: 165,006,829 (GRCm39)	A159V	possibly damaging	Het
Sh3gl1	G	T	17: 56,325,088 (GRCm39)	R250S	probably benign	Het
Skor1	C	A	9: 63,053,277 (GRCm39)	D231Y	probably damaging	Het
Slc24a1	T	G	9: 64,856,034 (GRCm39)	E291A	unknown	Het
Slc28a2b	G	T	2: 122,348,078 (GRCm39)		probably benign	Het
Smc1b	A	T	15: 84,951,925 (GRCm39)		probably benign	Het
Tbccd1	A	T	16: 22,644,844 (GRCm39)	N177K	possibly damaging	Het
Tdp1	T	A	12: 99,921,248 (GRCm39)	Y595N	probably damaging	Het
Tle5	G	A	10: 81,397,054 (GRCm39)	G10D	possibly damaging	Het
Tmem108	T	C	9: 103,366,504 (GRCm39)	K496E	possibly damaging	Het
Tmprss7	T	C	16: 45,487,959 (GRCm39)	D490G	probably damaging	Het
Tnrc6b	A	T	15: 80,802,729 (GRCm39)	N1511Y	probably damaging	Het
Top2b	G	A	14: 16,409,263 (GRCm38)	R802Q	probably damaging	Het
Trip10	A	T	17: 57,557,798 (GRCm39)	K27N	possibly damaging	Het
Txlnb	A	G	10: 17,718,503 (GRCm39)	N445D	possibly damaging	Het
Txnrd1	T	A	10: 82,715,636 (GRCm39)	I159N	probably damaging	Het
Ulk1	C	A	5: 110,944,193 (GRCm39)	A164S	probably null	Het
Vmn2r83	T	C	10: 79,327,798 (GRCm39)	V802A	probably damaging	Het
Zbtb4	A	G	11: 69,670,177 (GRCm39)	I967V	probably benign	Het

Other mutations in Necab3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00090:Necab3	APN	2	154,389,488 (GRCm39)	unclassified	probably benign
IGL01515:Necab3	APN	2	154,396,611 (GRCm39)	missense	probably damaging	1.00
IGL02438:Necab3	APN	2	154,387,964 (GRCm39)	missense	probably damaging	1.00
IGL03150:Necab3	APN	2	154,396,662 (GRCm39)	missense	probably damaging	1.00
R0102:Necab3	UTSW	2	154,387,232 (GRCm39)	missense	probably damaging	1.00
R0102:Necab3	UTSW	2	154,387,232 (GRCm39)	missense	probably damaging	1.00
R0219:Necab3	UTSW	2	154,388,013 (GRCm39)	missense	probably benign	0.17
R0656:Necab3	UTSW	2	154,388,223 (GRCm39)	missense	probably null	0.28
R1728:Necab3	UTSW	2	154,388,795 (GRCm39)	missense	probably benign	0.09
R1729:Necab3	UTSW	2	154,388,795 (GRCm39)	missense	probably benign	0.09
R2192:Necab3	UTSW	2	154,388,999 (GRCm39)	missense	possibly damaging	0.62
R4622:Necab3	UTSW	2	154,397,502 (GRCm39)	critical splice donor site	probably null
R5434:Necab3	UTSW	2	154,389,379 (GRCm39)	missense	probably damaging	1.00
R5577:Necab3	UTSW	2	154,387,076 (GRCm39)	splice site	probably null
R6603:Necab3	UTSW	2	154,396,842 (GRCm39)	missense	probably damaging	1.00
R7792:Necab3	UTSW	2	154,388,200 (GRCm39)	missense	probably damaging	1.00
R8195:Necab3	UTSW	2	154,389,363 (GRCm39)	missense	probably benign	0.05
R8831:Necab3	UTSW	2	154,396,607 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGCACTTGGAGTTTTGCCTCTAGC -3'
(R):5'- ATTGCCAGTGACTTCTGGGGTGAC -3'

Sequencing Primer
(F):5'- TTGCACAGCGATCTGAGAC -3'
(R):5'- TCTTCCAGGCGGGGAAAC -3'

Posted On

2013-04-11