Mutagenetix > Incidental Mutation

Incidental Mutation 'R3758:Nipa2'

271524

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

040739-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.885) question?

Stock #

R3758 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

55581035-55612224 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 55585689 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 102 (Y102C)

Ref Sequence

ENSEMBL: ENSMUSP00000114020 (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 damaging
Transcript: ENSMUST00000032635
AA Change: Y102C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000032635
Gene: ENSMUSG00000030452
AA Change: Y102C

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 damaging
Transcript: ENSMUST00000117812
AA Change: Y102C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000113727
Gene: ENSMUSG00000030452
AA Change: Y102C

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 damaging
Transcript: ENSMUST00000119041
AA Change: Y102C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000112394
Gene: ENSMUSG00000030452
AA Change: Y102C

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 damaging
Transcript: ENSMUST00000119201
AA Change: Y102C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000114020
Gene: ENSMUSG00000030452
AA Change: Y102C

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 damaging
Transcript: ENSMUST00000126604
AA Change: Y102C

PolyPhen 2 Score 0.958 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000116219
Gene: ENSMUSG00000030452
AA Change: Y102C

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 damaging
Transcript: ENSMUST00000152649
AA Change: Y83C

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000120798
Gene: ENSMUSG00000030452
AA Change: Y83C

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

Meta Mutation Damage Score

0.2664

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.0%
20x: 94.1%

Validation Efficiency

93% (28/30)

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: 30 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acat3	A	G	17: 13,146,354 (GRCm39)		probably benign	Het
Bcat1	T	A	6: 144,978,598 (GRCm39)	I208F	probably damaging	Het
Cage1	A	C	13: 38,209,705 (GRCm39)	F91V	possibly damaging	Het
Cd200r3	T	G	16: 44,784,991 (GRCm39)		probably null	Het
Coq8b	C	T	7: 26,941,652 (GRCm39)	Q246*	probably null	Het
Dmxl1	G	A	18: 50,068,384 (GRCm39)	G2719D	probably damaging	Het
Fbln2	T	C	6: 91,233,363 (GRCm39)	S616P	probably damaging	Het
Fkbp10	G	A	11: 100,313,451 (GRCm39)		probably null	Het
Gabra1	G	T	11: 42,066,763 (GRCm39)	D50E	probably benign	Het
H1f4	T	A	13: 23,806,240 (GRCm39)	K81*	probably null	Het
Hmgcs2	A	G	3: 98,198,406 (GRCm39)	N103S	probably damaging	Het
Htt	A	G	5: 35,053,314 (GRCm39)	H2549R	probably damaging	Het
Lrba	A	G	3: 86,683,356 (GRCm39)	E2726G	probably damaging	Het
Lrrc7	T	C	3: 157,869,602 (GRCm39)	N706D	probably damaging	Het
Mill1	G	A	7: 17,996,628 (GRCm39)		probably null	Het
Mtcl2	T	C	2: 156,862,558 (GRCm39)	N1457S	possibly damaging	Het
Nmd3	T	A	3: 69,631,641 (GRCm39)	C32*	probably null	Het
Or11h6	A	G	14: 50,880,493 (GRCm39)	K252E	possibly damaging	Het
Or4a78	A	G	2: 89,497,916 (GRCm39)	F105L	probably benign	Het
Or52r1b	A	G	7: 102,691,177 (GRCm39)	S159G	probably benign	Het
Or6c207	T	C	10: 129,104,934 (GRCm39)	D86G	probably damaging	Het
Pcdhb7	A	G	18: 37,476,079 (GRCm39)	D405G	possibly damaging	Het
Ptprt	A	T	2: 161,653,950 (GRCm39)	L560Q	probably damaging	Het
Serpinb9b	A	G	13: 33,219,571 (GRCm39)	Y166C	probably damaging	Het
Sprr1a	T	G	3: 92,391,704 (GRCm39)	K99T	probably damaging	Het
Spsb4	A	G	9: 96,877,924 (GRCm39)	V133A	probably damaging	Het
Suz12	A	G	11: 79,915,768 (GRCm39)	T391A	probably benign	Het
Tor1aip2	A	G	1: 155,941,035 (GRCm39)	E447G	probably damaging	Het
Ube4a	G	A	9: 44,861,198 (GRCm39)		probably benign	Het
Wdfy4	A	C	14: 32,745,331 (GRCm39)	H2296Q	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
R3870:Nipa2	UTSW	7	55,582,690 (GRCm39)	missense	probably damaging	1.00
R4684:Nipa2	UTSW	7	55,585,574 (GRCm39)	missense	probably benign
R4775:Nipa2	UTSW	7	55,585,611 (GRCm39)	missense	probably benign	0.19
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'- AGGGACACATGAGAACCATTTC -3'
(R):5'- TCTCAGTCAGATTGGTCAGGC -3'

Sequencing Primer
(F):5'- GAGAACCATTTCTTATAACCTGTGC -3'
(R):5'- CCTGCTAGTTGGATGCTCACAAATG -3'

Posted On

2015-03-18