Mutagenetix > Incidental Mutation

Incidental Mutation 'R6880:Nipa2'

536615

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

044976-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.854) question?

Stock #

R6880 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

55581035-55612224 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 55582999 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 249 (T249A)

Ref Sequence

ENSEMBL: ENSMUSP00000114020 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032629] [ENSMUST00000032635] [ENSMUST00000085255] [ENSMUST00000117812] [ENSMUST00000119041] [ENSMUST00000119201] [ENSMUST00000126604] [ENSMUST00000152649] [ENSMUST00000163845]

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: T249A

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000032635
Gene: ENSMUSG00000030452
AA Change: T249A

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: ENSMUST00000085255

SMART Domains

Protein: ENSMUSP00000082353
Gene: ENSMUSG00000030447

Domain	Start	End	E-Value	Type
low complexity region	15	27	N/A	INTRINSIC
Pfam:FragX_IP	385	1222	N/A	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000117812
AA Change: T249A

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000113727
Gene: ENSMUSG00000030452
AA Change: T249A

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: T249A

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000112394
Gene: ENSMUSG00000030452
AA Change: T249A

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: T249A

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000114020
Gene: ENSMUSG00000030452
AA Change: T249A

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

SMART Domains

Protein: ENSMUSP00000116219
Gene: ENSMUSG00000030452

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

probably benign
Transcript: ENSMUST00000152649

SMART Domains

Protein: ENSMUSP00000120798
Gene: ENSMUSG00000030452

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

Predicted Effect

probably benign
Transcript: ENSMUST00000163845

SMART Domains

Protein: ENSMUSP00000127717
Gene: ENSMUSG00000030447

Domain	Start	End	E-Value	Type
low complexity region	15	27	N/A	INTRINSIC
Pfam:FragX_IP	385	1224	N/A	PFAM

Meta Mutation Damage Score

0.2805

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.1%

Validation Efficiency

97% (62/64)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad9	T	A	3: 36,123,854 (GRCm39)		probably null	Het
Aff3	T	C	1: 38,574,243 (GRCm39)	H206R	probably damaging	Het
Aff3	T	C	1: 38,666,209 (GRCm39)	D5G	possibly damaging	Het
Alg5	A	G	3: 54,646,264 (GRCm39)	E43G	probably damaging	Het
Ankrd36	T	C	11: 5,578,748 (GRCm39)	L4P	probably damaging	Het
Ano1	T	C	7: 144,198,479 (GRCm39)	Y345C	probably benign	Het
Atf7ip	A	G	6: 136,538,038 (GRCm39)	I432V	probably damaging	Het
B230307C23Rik	T	C	16: 97,798,627 (GRCm39)		probably benign	Het
Baz2b	T	A	2: 59,743,283 (GRCm39)	N1563Y	probably damaging	Het
Bhlha15	A	T	5: 144,128,451 (GRCm39)	T188S	probably damaging	Het
Cbr3	T	C	16: 93,487,426 (GRCm39)	V203A	probably benign	Het
Cpsf1	T	C	15: 76,486,739 (GRCm39)	T266A	probably benign	Het
Dnah7c	T	C	1: 46,566,831 (GRCm39)	Y681H	probably damaging	Het
Dock2	C	T	11: 34,579,279 (GRCm39)		probably null	Het
Dsc1	T	A	18: 20,221,429 (GRCm39)	D682V	probably damaging	Het
Fkbp15	A	T	4: 62,254,732 (GRCm39)	I256N	possibly damaging	Het
Foxd1	A	C	13: 98,491,225 (GRCm39)	D33A	unknown	Het
Gid4	T	A	11: 60,327,261 (GRCm39)	F149I	probably damaging	Het
Hmcn2	G	T	2: 31,233,068 (GRCm39)	V206L	probably damaging	Het
Ighg2b	T	C	12: 113,270,726 (GRCm39)	I135V		Het
Ighv1-24	T	C	12: 114,736,663 (GRCm39)	Y79C	possibly damaging	Het
Impg1	T	A	9: 80,312,082 (GRCm39)	D167V	probably damaging	Het
Jakmip1	T	C	5: 37,262,967 (GRCm39)	S372P	possibly damaging	Het
Kcnb1	T	C	2: 166,947,727 (GRCm39)	T374A	probably damaging	Het
Lrrn4	A	G	2: 132,714,032 (GRCm39)	S305P	probably damaging	Het
Ltbp1	C	T	17: 75,628,044 (GRCm39)	T1179I	possibly damaging	Het
Mab21l2	A	G	3: 86,454,463 (GRCm39)	I179T	possibly damaging	Het
Myo5b	A	T	18: 74,855,501 (GRCm39)	H1230L	probably benign	Het
Myocos	T	C	1: 162,484,602 (GRCm39)		probably null	Het
Oas1a	C	A	5: 121,040,003 (GRCm39)	R196L	probably damaging	Het
Or2ag18	A	T	7: 106,405,019 (GRCm39)	S217T	probably damaging	Het
Or5an11	A	G	19: 12,245,974 (GRCm39)	I127V	probably benign	Het
Or8k41	A	G	2: 86,314,069 (GRCm39)	F6L	probably benign	Het
Phxr2	G	A	10: 98,961,946 (GRCm39)		probably benign	Het
Pigq	A	G	17: 26,153,802 (GRCm39)	L85P	probably damaging	Het
Pla2g4a	T	A	1: 149,727,202 (GRCm39)	D518V	possibly damaging	Het
Pm20d1	A	G	1: 131,731,839 (GRCm39)	K294E	probably benign	Het
Polr3d	C	A	14: 70,677,455 (GRCm39)	R307L	probably benign	Het
Pou5f2	T	C	13: 78,173,613 (GRCm39)	L185P	possibly damaging	Het
Prex2	A	T	1: 11,202,608 (GRCm39)	N506Y	probably damaging	Het
Proser1	T	A	3: 53,385,260 (GRCm39)	S381T	probably benign	Het
Prpf4b	T	C	13: 35,078,436 (GRCm39)	V682A	possibly damaging	Het
Prr14l	A	T	5: 32,988,211 (GRCm39)	L428Q	probably benign	Het
Prss23	A	G	7: 89,160,033 (GRCm39)	V12A	probably benign	Het
Qki	T	C	17: 10,434,376 (GRCm39)	D321G	probably benign	Het
Rab11fip5	A	G	6: 85,325,827 (GRCm39)	L193P	probably damaging	Het
Retreg1	T	G	15: 25,971,825 (GRCm39)	L245R	probably damaging	Het
Rfc1	T	C	5: 65,434,729 (GRCm39)	N679S	probably benign	Het
Rpl4	C	T	9: 64,084,335 (GRCm39)	A220V	probably damaging	Het
Rxra	G	A	2: 27,638,668 (GRCm39)	E224K	possibly damaging	Het
Slc26a7	A	G	4: 14,516,159 (GRCm39)	C557R	possibly damaging	Het
Sncaip	A	G	18: 53,002,136 (GRCm39)	K219R	probably damaging	Het
Sorbs1	G	C	19: 40,365,244 (GRCm39)	R180G	probably benign	Het
Sphkap	A	G	1: 83,234,978 (GRCm39)	V1616A	probably damaging	Het
Sulf1	T	C	1: 12,912,979 (GRCm39)	C738R	probably damaging	Het
Suz12	T	A	11: 79,892,998 (GRCm39)	C38*	probably null	Het
Ttn	T	C	2: 76,550,842 (GRCm39)	T23190A	probably damaging	Het
Twnk	A	G	19: 44,995,855 (GRCm39)	D96G	probably benign	Het
Vcan	T	A	13: 89,860,500 (GRCm39)	N289I	probably damaging	Het
Vmn2r120	A	T	17: 57,816,187 (GRCm39)	S723T	probably damaging	Het
Vmn2r97	A	T	17: 19,134,770 (GRCm39)	I63F	probably benign	Het
Washc5	T	C	15: 59,222,021 (GRCm39)	N125S	probably benign	Het
Zfp865	A	G	7: 5,033,548 (GRCm39)	Y511C	probably damaging	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
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
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'- ACTAGAAAGATTGCCATTCATTGCC -3'
(R):5'- AGCATTTTCAGTCTCCTGTGTG -3'

Sequencing Primer
(F):5'- GCAGACTTGCTAGACTAAAACTG -3'
(R):5'- CAGTCTCCTGTGTGAAGGG -3'

Posted On

2018-10-18