Mutagenetix > Incidental Mutations

Incidental Mutation 'R4794:Ndc1'

404197

Institutional Source

Beutler Lab

Gene Symbol

Ndc1

Ensembl Gene

ENSMUSG00000028614

Gene Name

NDC1 transmembrane nucleoporin

Synonyms

sks, Tmem48, 2810475A17Rik

MMRRC Submission

042420-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.935) question?

Stock #

R4794 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

107367784-107416346 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 107390222 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 409 (E409G)

Ref Sequence

ENSEMBL: ENSMUSP00000137180 (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 benign
Transcript: ENSMUST00000139560
AA Change: E409G

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000120365
Gene: ENSMUSG00000028614
AA Change: E409G

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

Predicted Effect

probably benign
Transcript: ENSMUST00000149366
AA Change: E409G

PolyPhen 2 Score 0.030 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000137180
Gene: ENSMUSG00000028614
AA Change: E409G

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150800

Meta Mutation Damage Score

0.0644

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 92.5%

Validation Efficiency

97% (75/77)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam4	A	T	12: 81,421,424	I141K	probably damaging	Het
Adgrb1	A	G	15: 74,588,129	E537G	probably damaging	Het
Asic3	C	T	5: 24,415,897	A259V	probably damaging	Het
Bcar1	G	A	8: 111,720,920	Q142*	probably null	Het
Bcas3	T	C	11: 85,509,468	V200A	probably damaging	Het
Cd302	A	T	2: 60,272,149	I42N	probably benign	Het
Colec12	C	A	18: 9,848,984	N387K	probably damaging	Het
Copa	T	A	1: 172,119,321	I1032N	probably damaging	Het
D630003M21Rik	G	C	2: 158,196,139	T1129S	probably benign	Het
D630045J12Rik	G	A	6: 38,194,485	T916I	possibly damaging	Het
Dnajb13	C	T	7: 100,503,992	A241T	probably damaging	Het
Dyrk4	G	T	6: 126,885,337	N397K	possibly damaging	Het
Eftud2	T	A	11: 102,870,177	Y114F	probably benign	Het
Epm2a	A	G	10: 11,390,853	D114G	probably benign	Het
Exoc5	T	C	14: 49,048,900		probably null	Het
Fam135a	G	A	1: 24,029,160	T706I	probably benign	Het
Fasn	A	G	11: 120,811,295	V1845A	probably benign	Het
Fscn3	A	G	6: 28,430,596	E255G	probably damaging	Het
Galnt7	A	T	8: 57,545,363	Y311N	probably damaging	Het
Gm13757	A	T	2: 88,446,347	M197K	probably benign	Het
Gm5724	A	G	6: 141,767,562	V31A	probably benign	Het
Gm8765	C	G	13: 50,703,239	P971R	probably benign	Het
Grid1	T	C	14: 34,822,622	L50P	probably damaging	Het
Hepacam2	A	G	6: 3,475,933	F331L	probably damaging	Het
Ikbkap	ACTTCTTCTTCTTCTTCTTCTTC	ACTTCTTCTTCTTCTTCTTC	4: 56,781,176		probably benign	Het
Kalrn	C	T	16: 33,989,810	D2525N	possibly damaging	Het
Kif1a	T	C	1: 93,025,727	Y1245C	probably damaging	Het
Ltbp3	T	C	19: 5,756,679	F1022L	probably damaging	Het
Med16	G	T	10: 79,900,117	T399N	probably damaging	Het
Mfsd14a	A	T	3: 116,645,506		probably benign	Het
Myh7b	G	A	2: 155,623,266	V681I	probably benign	Het
Necap2	A	G	4: 141,071,601		probably benign	Het
Olfr47	T	A	6: 43,235,695	L29H	probably damaging	Het
Olfr847	C	T	9: 19,375,545	S112N	probably benign	Het
Parp12	G	A	6: 39,117,810	T117I	probably benign	Het
Pars2	C	A	4: 106,654,210	C396*	probably null	Het
Prg4	A	T	1: 150,454,546		probably benign	Het
Prkg2	G	A	5: 98,966,633	T523I	probably damaging	Het
Prph	T	A	15: 99,057,427	L425Q	probably damaging	Het
Ranbp9	A	G	13: 43,414,076	Y549H	probably damaging	Het
Rbm12	A	T	2: 156,095,569		probably benign	Het
Reln	T	C	5: 22,344,185	Y75C	probably damaging	Het
Rock2	G	A	12: 16,940,407	R110H	probably damaging	Het
Samd1	G	A	8: 83,999,717	E468K	probably damaging	Het
Samd11	T	A	4: 156,249,465	Q173L	probably damaging	Het
Scgb2b20	C	A	7: 33,365,726	G37V	probably damaging	Het
Sf1	C	A	19: 6,375,664		probably benign	Het
Slc17a5	T	A	9: 78,574,715	H183L	probably damaging	Het
Smgc	T	A	15: 91,841,454	S13T	probably benign	Het
Snapin	A	G	3: 90,490,785		probably benign	Het
Ssc5d	C	T	7: 4,943,745	P1033S	probably benign	Het
Strn3	T	C	12: 51,650,171	E259G	probably benign	Het
Tbc1d32	A	G	10: 56,196,836	F238L	possibly damaging	Het
Tbck	G	A	3: 132,686,968	V57M	possibly damaging	Het
Tgm3	A	G	2: 130,041,955	D511G	probably benign	Het
Tlr5	T	C	1: 182,973,896	V241A	probably benign	Het
Tmem181c-ps	A	G	17: 6,620,355		noncoding transcript	Het
Tnfrsf1a	G	A	6: 125,358,084	C168Y	probably damaging	Het
Tph2	G	T	10: 115,182,770	L79I	possibly damaging	Het
Tsc1	G	A	2: 28,661,690		probably null	Het
Ttc14	A	T	3: 33,803,149	M215L	probably benign	Het
Ube3c	A	G	5: 29,597,085	N120S	probably benign	Het
Ubr2	A	T	17: 46,930,445	W1728R	probably damaging	Het
Vnn1	A	G	10: 23,900,704	T318A	probably benign	Het
Washc2	T	C	6: 116,258,649	V941A	probably benign	Het
Wdfy3	A	G	5: 101,943,943	V510A	probably damaging	Het
Wdsub1	A	T	2: 59,862,844	V272E	possibly damaging	Het
Xylt1	A	C	7: 117,637,635	D537A	probably benign	Het
Zfp57	A	G	17: 37,010,130	N292S	possibly damaging	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
R3522:Ndc1	UTSW	4	107393158	missense	probably damaging	0.99
R4036:Ndc1	UTSW	4	107411072	missense	probably benign	0.22
R4698:Ndc1	UTSW	4	107411137	missense	probably benign	0.06
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
Z1176:Ndc1	UTSW	4	107386602	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- ACTCCTTGAGTGGTTTCTGGATTAC -3'
(R):5'- CTCTTCTTATGAGCTGAGGACTTTG -3'

Sequencing Primer
(F):5'- GCCATCTACTGTGCTTTG -3'
(R):5'- CCCAGAGAAGGGGTTTACATC -3'

Posted On

2016-07-22