Mutagenetix > Incidental Mutation

Incidental Mutation 'R4775:Nipa2'

367845

Institutional Source

Beutler Lab

Gene Symbol

Nipa2

Ensembl Gene

ENSMUSG00000030452

Gene Name

non imprinted in Prader-Willi/Angelman syndrome 2 homolog (human)

Synonyms

3830408P04Rik, 2600017P10Rik

MMRRC Submission

041991-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.854) question?

Stock #

R4775 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

55581035-55612224 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 55585611 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 109 (I109T)

Ref Sequence

ENSEMBL: ENSMUSP00000120798 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032629] [ENSMUST00000032635] [ENSMUST00000117812] [ENSMUST00000119041] [ENSMUST00000119201] [ENSMUST00000126604] [ENSMUST00000152649]

AlphaFold

Q9JJC8

Predicted Effect

probably benign
Transcript: ENSMUST00000032629

SMART Domains

Protein: ENSMUSP00000032629
Gene: ENSMUSG00000030447

Domain	Start	End	E-Value	Type
low complexity region	15	27	N/A	INTRINSIC
Pfam:DUF1394	59	302	5.7e-11	PFAM
Pfam:FragX_IP	389	1222	N/A	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000032635
AA Change: I128T

PolyPhen 2 Score 0.146 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000032635
Gene: ENSMUSG00000030452
AA Change: I128T

Domain	Start	End	E-Value	Type
Pfam:Mg_trans_NIPA	6	306	3.2e-150	PFAM
Pfam:EmrE	16	135	6.2e-12	PFAM
Pfam:EamA	52	128	9.5e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000117812
AA Change: I128T

PolyPhen 2 Score 0.146 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000113727
Gene: ENSMUSG00000030452
AA Change: I128T

Domain	Start	End	E-Value	Type
Pfam:Mg_trans_NIPA	8	302	1.4e-151	PFAM
Pfam:EamA	47	128	4.3e-12	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000119041
AA Change: I128T

PolyPhen 2 Score 0.146 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000112394
Gene: ENSMUSG00000030452
AA Change: I128T

Domain	Start	End	E-Value	Type
Pfam:Mg_trans_NIPA	6	306	3.2e-150	PFAM
Pfam:EmrE	16	135	6.2e-12	PFAM
Pfam:EamA	52	128	9.5e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000119201
AA Change: I128T

PolyPhen 2 Score 0.146 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000114020
Gene: ENSMUSG00000030452
AA Change: I128T

Domain	Start	End	E-Value	Type
Pfam:Mg_trans_NIPA	6	306	3.2e-150	PFAM
Pfam:EmrE	16	135	6.2e-12	PFAM
Pfam:EamA	52	128	9.5e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000126604
AA Change: I128T

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000116219
Gene: ENSMUSG00000030452
AA Change: I128T

Domain	Start	End	E-Value	Type
Pfam:Mg_trans_NIPA	6	130	1.2e-66	PFAM
Pfam:EmrE	14	130	1.8e-11	PFAM
Pfam:EamA	50	128	1.8e-11	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130239

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147950

Predicted Effect

probably benign
Transcript: ENSMUST00000152649
AA Change: I109T

PolyPhen 2 Score 0.193 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000120798
Gene: ENSMUSG00000030452
AA Change: I109T

Domain	Start	End	E-Value	Type
Pfam:Mg_trans_NIPA	6	127	1.9e-53	PFAM
Pfam:EamA	10	109	1.8e-9	PFAM
Pfam:EmrE	18	116	1.1e-8	PFAM

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.6%
20x: 93.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a possible magnesium transporter. This gene is located adjacent to the imprinted domain in the Prader-Willi syndrome deletion region of chromosome 15. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 3, 7 and 21.[provided by RefSeq, May 2010]

Allele List at MGI

Other mutations in this stock

Total: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	A	G	11: 84,134,165 (GRCm39)	Y426C	probably damaging	Het
Adam7	A	G	14: 68,745,361 (GRCm39)	I621T	probably benign	Het
Adamts1	A	T	16: 85,597,278 (GRCm39)	Y260*	probably null	Het
Adgrf1	C	T	17: 43,622,054 (GRCm39)	L764F	probably damaging	Het
Afg3l2	G	T	18: 67,554,329 (GRCm39)	L458M	probably damaging	Het
Atp9b	A	G	18: 80,808,984 (GRCm39)		probably null	Het
C5ar2	A	C	7: 15,971,540 (GRCm39)	L129R	probably damaging	Het
Ccdc174	G	A	6: 91,867,875 (GRCm39)		probably null	Het
Cidec	T	C	6: 113,411,695 (GRCm39)	M1V	probably null	Het
Clec16a	G	T	16: 10,456,778 (GRCm39)	R663L	probably damaging	Het
Col25a1	T	C	3: 129,976,468 (GRCm39)	C118R	possibly damaging	Het
Cox6b2	A	G	7: 4,755,074 (GRCm39)	C67R	probably damaging	Het
Cspg4b	A	T	13: 113,454,229 (GRCm39)	I92F	possibly damaging	Het
Cwf19l2	A	G	9: 3,430,973 (GRCm39)	Y435C	probably benign	Het
Dapk1	T	A	13: 60,897,156 (GRCm39)	S792T	probably benign	Het
Dis3l	T	A	9: 64,238,190 (GRCm39)	N101Y	probably benign	Het
Dsg4	A	G	18: 20,604,184 (GRCm39)	T884A	possibly damaging	Het
Dvl1	T	C	4: 155,942,584 (GRCm39)	W617R	probably benign	Het
Eml5	A	G	12: 98,768,566 (GRCm39)	V1503A	probably benign	Het
Engase	A	T	11: 118,373,497 (GRCm39)	D280V	probably benign	Het
F11r	T	C	1: 171,289,209 (GRCm39)	S224P	probably damaging	Het
Fanca	A	G	8: 124,023,045 (GRCm39)	V564A	probably damaging	Het
Foxj2	G	T	6: 122,810,230 (GRCm39)	Q196H	probably benign	Het
Gle1	T	C	2: 29,826,073 (GRCm39)	W51R	possibly damaging	Het
Gm94	A	G	18: 43,925,836 (GRCm39)		probably null	Het
Gm9830	A	T	9: 44,375,721 (GRCm39)		noncoding transcript	Het
Gpaa1	T	A	15: 76,218,891 (GRCm39)		probably null	Het
Grin1	C	T	2: 25,182,475 (GRCm39)	A929T	possibly damaging	Het
Grm7	T	A	6: 110,891,332 (GRCm39)	D188E	probably damaging	Het
Gtf2ird2	T	C	5: 134,242,970 (GRCm39)	F395L	probably benign	Het
Lipo3	C	A	19: 33,757,795 (GRCm39)	G225C	probably damaging	Het
Lonrf2	T	A	1: 38,857,140 (GRCm39)		probably null	Het
Marveld2	A	G	13: 100,753,303 (GRCm39)		probably benign	Het
Mpl	A	G	4: 118,305,777 (GRCm39)	L416P	probably damaging	Het
Mppe1	A	G	18: 67,359,930 (GRCm39)	L312P	possibly damaging	Het
Mpzl3	T	A	9: 44,977,730 (GRCm39)	S113T	probably damaging	Het
Mylk3	G	A	8: 86,085,689 (GRCm39)	Q149*	probably null	Het
Myt1	T	A	2: 181,464,470 (GRCm39)	I968N	probably damaging	Het
Ndc80	A	G	17: 71,821,265 (GRCm39)	Y228H	probably damaging	Het
Nelfcd	T	G	2: 174,268,369 (GRCm39)	C520G	probably damaging	Het
Nfrkb	C	A	9: 31,330,345 (GRCm39)	T1199K	possibly damaging	Het
Nlrp4e	A	G	7: 23,042,525 (GRCm39)	T804A	probably benign	Het
Nsf	A	T	11: 103,763,419 (GRCm39)	I395K	possibly damaging	Het
Nt5c1b	G	A	12: 10,425,449 (GRCm39)	V331I	probably damaging	Het
Or13a28	A	T	7: 140,217,829 (GRCm39)	I72F	probably damaging	Het
Or1e29	A	G	11: 73,667,377 (GRCm39)	Y259H	probably damaging	Het
Pask	T	C	1: 93,265,246 (GRCm39)	D3G	probably damaging	Het
Pglyrp3	T	C	3: 91,933,037 (GRCm39)	V110A	possibly damaging	Het
Ppp4r3a	C	T	12: 101,019,825 (GRCm39)	V377M	probably damaging	Het
Prr12	A	G	7: 44,700,749 (GRCm39)		probably benign	Het
Ptdss1	G	A	13: 67,135,922 (GRCm39)		probably null	Het
Qser1	A	G	2: 104,620,246 (GRCm39)	S189P	probably damaging	Het
Rph3a	T	A	5: 121,092,551 (GRCm39)	Y350F	probably benign	Het
Skint4	A	T	4: 111,993,261 (GRCm39)	H328L	probably damaging	Het
Smyd4	G	A	11: 75,282,018 (GRCm39)	C497Y	probably damaging	Het
Stk11ip	T	C	1: 75,510,497 (GRCm39)	W864R	possibly damaging	Het
Stkld1	T	A	2: 26,841,757 (GRCm39)	V543E	probably damaging	Het
Taok2	A	G	7: 126,469,940 (GRCm39)	S963P	probably damaging	Het
Tars2	A	G	3: 95,653,959 (GRCm39)	L354P	probably damaging	Het
Tns2	C	T	15: 102,017,369 (GRCm39)	R281C	probably damaging	Het
Tpcn2	A	G	7: 144,821,079 (GRCm39)	L325P	probably damaging	Het
Trappc3l	C	G	10: 33,974,807 (GRCm39)	H96Q	probably benign	Het
Trim66	A	T	7: 109,056,796 (GRCm39)	Y1120*	probably null	Het
Trio	G	A	15: 27,881,428 (GRCm39)	Q548*	probably null	Het
Wipf2	T	A	11: 98,781,558 (GRCm39)	D32E	probably benign	Het

Other mutations in Nipa2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01105:Nipa2	APN	7	55,583,193 (GRCm39)	missense	probably damaging	1.00
IGL01965:Nipa2	APN	7	55,594,371 (GRCm39)	start gained	probably benign
IGL02373:Nipa2	APN	7	55,582,876 (GRCm39)	missense	probably benign	0.01
IGL02812:Nipa2	APN	7	55,592,766 (GRCm39)	missense	probably damaging	1.00
IGL03079:Nipa2	APN	7	55,583,205 (GRCm39)	missense	probably damaging	1.00
IGL03188:Nipa2	APN	7	55,582,680 (GRCm39)	missense	probably benign
R1327:Nipa2	UTSW	7	55,594,256 (GRCm39)	missense	possibly damaging	0.81
R2356:Nipa2	UTSW	7	55,582,714 (GRCm39)	missense	probably benign	0.00
R3758:Nipa2	UTSW	7	55,585,689 (GRCm39)	missense	probably damaging	1.00
R3870:Nipa2	UTSW	7	55,582,690 (GRCm39)	missense	probably damaging	1.00
R4684:Nipa2	UTSW	7	55,585,574 (GRCm39)	missense	probably benign
R5285:Nipa2	UTSW	7	55,582,760 (GRCm39)	nonsense	probably null
R6453:Nipa2	UTSW	7	55,585,569 (GRCm39)	missense	probably damaging	0.98
R6880:Nipa2	UTSW	7	55,582,999 (GRCm39)	missense	probably damaging	0.99
R7459:Nipa2	UTSW	7	55,583,089 (GRCm39)	missense	probably damaging	1.00
R8312:Nipa2	UTSW	7	55,583,050 (GRCm39)	nonsense	probably null
R8835:Nipa2	UTSW	7	55,583,307 (GRCm39)	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- TCGGATAATGACTTTGGCTAAGG -3'
(R):5'- CAGTGATCTGCATTGCAAGTCTG -3'

Sequencing Primer
(F):5'- GCTAGGGACACATGAGAACCATTTC -3'
(R):5'- CTGCATTGCAAGTCTGTTAATTTTC -3'

Posted On

2015-12-29