Mutagenetix > Incidental Mutation

Incidental Mutation 'R3522:Ndc1'

267526

Institutional Source

Beutler Lab

Gene Symbol

Ndc1

Ensembl Gene

ENSMUSG00000028614

Gene Name

NDC1 transmembrane nucleoporin

Synonyms

sks, Tmem48, 2810475A17Rik

Accession Numbers

Essential gene?

Probably essential (E-score: 0.949) question?

Stock #

R3522 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

107367784-107416346 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 107393158 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 533 (S533P)

Ref Sequence

ENSEMBL: ENSMUSP00000120365 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030357] [ENSMUST00000125342] [ENSMUST00000139560] [ENSMUST00000149366]

AlphaFold

Q8VCB1

Predicted Effect

probably benign
Transcript: ENSMUST00000030357

Predicted Effect

probably benign
Transcript: ENSMUST00000125342

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132950

Predicted Effect

probably damaging
Transcript: ENSMUST00000139560
AA Change: S533P

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000120365
Gene: ENSMUSG00000028614
AA Change: S533P

Domain	Start	End	E-Value	Type
Pfam:Ndc1_Nup	20	666	1.7e-137	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000149366

SMART Domains

Protein: ENSMUSP00000137180
Gene: ENSMUSG00000028614

Domain	Start	End	E-Value	Type
Pfam:Ndc1_Nup	19	511	3.7e-136	PFAM

Meta Mutation Damage Score

0.4043

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.2%
20x: 94.8%

Validation Efficiency

100% (72/72)

MGI Phenotype

PHENOTYPE: Mutations in this gene produce background sensitive growth rates and skeletal anomalies. Both females and males are sterile. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931409K22Rik	A	G	5: 24,549,626		probably null	Het
Ankrd35	A	G	3: 96,685,062	E888G	probably damaging	Het
Arhgef10	T	C	8: 14,954,918	F150S	probably damaging	Het
Atp10d	G	T	5: 72,239,157	R235L	probably benign	Het
Cacna1b	A	G	2: 24,763,043	V2A	possibly damaging	Het
Cand1	A	T	10: 119,239,197	L15Q	probably benign	Het
Cavin3	C	A	7: 105,481,143	G154V	probably benign	Het
Ccdc73	A	T	2: 104,991,485	D593V	probably damaging	Het
Cdk5rap2	T	C	4: 70,250,410	K161E	probably damaging	Het
Chil4	A	T	3: 106,203,740	N279K	probably benign	Het
Chst13	T	G	6: 90,318,263	D56A	probably damaging	Het
Cnn1	C	A	9: 22,099,368	H5N	probably benign	Het
Cpsf4l	T	A	11: 113,702,493	K88N	probably damaging	Het
Ctnnbl1	G	T	2: 157,871,193		probably null	Het
Dnah7a	A	C	1: 53,618,116	F834V	probably damaging	Het
Fbxo41	A	G	6: 85,484,181	S182P	probably benign	Het
Fkbp5	T	C	17: 28,415,996	T180A	probably benign	Het
Flg2	T	A	3: 93,220,027	I2082N	unknown	Het
Gm4968	A	G	6: 127,233,762		noncoding transcript	Het
Gpc5	T	A	14: 116,524,335	H612Q	probably benign	Het
Gsg1	A	T	6: 135,241,253	V212D	probably damaging	Het
Hipk1	A	G	3: 103,744,114	V1111A	probably damaging	Het
Hormad1	A	T	3: 95,576,285	Q136L	probably benign	Het
Ifi35	T	A	11: 101,457,685	S147R	probably benign	Het
Iqgap3	C	T	3: 88,090,782	A282V	probably null	Het
Jmy	T	C	13: 93,454,050	D515G	probably damaging	Het
Kctd10	G	A	5: 114,374,923	R64C	probably damaging	Het
Kidins220	T	C	12: 24,990,758	V121A	probably damaging	Het
Lcn3	G	A	2: 25,766,121	V63M	possibly damaging	Het
Lmx1b	T	A	2: 33,639,531	Y72F	probably benign	Het
Lrp1	T	C	10: 127,553,555	D3164G	probably damaging	Het
Mdh1b	C	T	1: 63,719,768	V222M	probably damaging	Het
Mst1	T	C	9: 108,081,503		probably benign	Het
Myo7b	C	A	18: 32,010,079	V189F	probably damaging	Het
Ndrg3	T	C	2: 156,944,027	D164G	probably damaging	Het
Nol11	C	T	11: 107,173,628	C500Y	possibly damaging	Het
Nsd3	A	G	8: 25,706,614	N1208D	probably benign	Het
Nup155	C	T	15: 8,156,678		probably benign	Het
Olfr768	A	G	10: 129,093,842	I44T	possibly damaging	Het
Olfr911-ps1	A	G	9: 38,523,785	T18A	probably damaging	Het
Olfr921	A	T	9: 38,775,720	D155V	possibly damaging	Het
Olfr988	A	T	2: 85,353,003	C308S	probably benign	Het
Phf3	A	G	1: 30,805,603	L1425P	probably damaging	Het
Pla2r1	A	G	2: 60,448,906	Y777H	probably damaging	Het
Pld1	A	G	3: 28,031,247	E184G	probably damaging	Het
Plxna1	T	C	6: 89,337,353		probably null	Het
Ptgfrn	T	C	3: 101,043,402	E865G	probably damaging	Het
Ptpn13	G	T	5: 103,589,854		probably benign	Het
Pygb	G	T	2: 150,828,553	V763F	probably benign	Het
Ros1	A	C	10: 52,090,995	Y1705*	probably null	Het
Sec61a2	A	G	2: 5,893,216	F5L	probably benign	Het
Skint5	A	G	4: 113,756,905		probably null	Het
Sntg2	A	G	12: 30,312,567	V60A	probably damaging	Het
Sppl2a	A	G	2: 126,920,322	C280R	possibly damaging	Het
Srrm4	A	C	5: 116,446,544	M1R	probably null	Het
Sult1c1	T	C	17: 53,972,015	E91G	probably damaging	Het
Themis2	C	G	4: 132,785,595	R440P	probably damaging	Het
Tmem229a	A	G	6: 24,955,059	L232P	probably benign	Het
Trappc1	T	C	11: 69,324,422	F43L	probably damaging	Het
Trappc11	A	T	8: 47,498,673	Y982N	possibly damaging	Het
Trpv6	A	T	6: 41,627,405	M139K	probably damaging	Het
Txnrd3	A	G	6: 89,663,075		probably null	Het
Vmn1r184	T	A	7: 26,267,583	Y251*	probably null	Het
Vmn1r216	A	G	13: 23,099,374	N76D	possibly damaging	Het
Vmn1r71	C	A	7: 10,747,865	V233F	probably benign	Het
Vps13a	A	C	19: 16,766,493		probably benign	Het
Vwa5b2	A	G	16: 20,601,608	S756G	probably damaging	Het
Wdr36	T	A	18: 32,861,485		probably null	Het
Wdr86	A	G	5: 24,718,307	V129A	probably benign	Het
Zfyve9	A	G	4: 108,719,743	L47S	probably benign	Het

Other mutations in Ndc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00927:Ndc1	APN	4	107384780	splice site	probably benign
IGL00929:Ndc1	APN	4	107389497	missense	probably benign	0.23
IGL01340:Ndc1	APN	4	107374147	missense	probably damaging	1.00
IGL01376:Ndc1	APN	4	107375197	missense	probably damaging	1.00
IGL01954:Ndc1	APN	4	107395804	missense	probably damaging	1.00
IGL02290:Ndc1	APN	4	107394995	splice site	probably benign
IGL03251:Ndc1	APN	4	107380659	missense	possibly damaging	0.50
R1168:Ndc1	UTSW	4	107395812	missense	probably benign	0.02
R1541:Ndc1	UTSW	4	107371288	nonsense	probably null
R1605:Ndc1	UTSW	4	107368096	missense	probably damaging	0.96
R1612:Ndc1	UTSW	4	107395068	splice site	probably benign
R1716:Ndc1	UTSW	4	107384795	missense	probably damaging	1.00
R4036:Ndc1	UTSW	4	107411072	missense	probably benign	0.22
R4698:Ndc1	UTSW	4	107411137	missense	probably benign	0.06
R4794:Ndc1	UTSW	4	107390222	missense	probably benign	0.03
R5053:Ndc1	UTSW	4	107374218	missense	probably damaging	1.00
R5097:Ndc1	UTSW	4	107374161	missense	probably benign	0.01
R5158:Ndc1	UTSW	4	107375165	missense	probably damaging	1.00
R5217:Ndc1	UTSW	4	107389576	missense	probably benign
R5579:Ndc1	UTSW	4	107380704	missense	possibly damaging	0.74
R5666:Ndc1	UTSW	4	107389526	missense	possibly damaging	0.52
R5855:Ndc1	UTSW	4	107383707	missense	probably damaging	1.00
R6180:Ndc1	UTSW	4	107411198	missense	possibly damaging	0.65
R6525:Ndc1	UTSW	4	107368107	missense	probably benign	0.01
R8065:Ndc1	UTSW	4	107390398	missense	probably benign	0.01
R8067:Ndc1	UTSW	4	107390398	missense	probably benign	0.01
R8100:Ndc1	UTSW	4	107383605	missense	possibly damaging	0.94
R8428:Ndc1	UTSW	4	107368820	missense	probably benign	0.00
R8952:Ndc1	UTSW	4	107390426	missense	probably benign	0.00
R8953:Ndc1	UTSW	4	107381693	missense	probably damaging	1.00
R9489:Ndc1	UTSW	4	107390666	critical splice donor site	probably null
R9606:Ndc1	UTSW	4	107389489	missense	probably damaging	0.97
Z1176:Ndc1	UTSW	4	107386602	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- CAAGGATCTAATTGGTGTCCAGTG -3'
(R):5'- ACATGTGTGTCTGGGCAGAG -3'

Sequencing Primer
(F):5'- CACAGTCACGGTAAGATGGCTC -3'
(R):5'- GGACACGATGCCAGCATG -3'

Posted On

2015-02-18