Mutagenetix > Incidental Mutation

Incidental Mutation 'R5217:Ndc1'

403521

Institutional Source

Beutler Lab

Gene Symbol

Ndc1

Ensembl Gene

ENSMUSG00000028614

Gene Name

NDC1 transmembrane nucleoporin

Synonyms

sks, 2810475A17Rik, Tmem48

MMRRC Submission

042790-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.943) question?

Stock #

R5217 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

107225244-107273543 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 107246773 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 399 (S399P)

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: S399P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000120365
Gene: ENSMUSG00000028614
AA Change: S399P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000149366
AA Change: S399P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000137180
Gene: ENSMUSG00000028614
AA Change: S399P

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

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 93.7%

Validation Efficiency

100% (80/80)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933428M09Rik	G	T	X: 138,080,282 (GRCm39)	G16*	probably null	Het
Abhd11	T	A	5: 135,040,398 (GRCm39)	W144R	probably damaging	Het
Abhd2	A	G	7: 78,973,378 (GRCm39)	E119G	probably benign	Het
Acbd3	A	G	1: 180,553,938 (GRCm39)	Y91C	probably benign	Het
Aox4	C	A	1: 58,285,400 (GRCm39)	S628*	probably null	Het
Bahcc1	T	A	11: 120,165,285 (GRCm39)	Y905*	probably null	Het
Baiap2l2	T	G	15: 79,154,687 (GRCm39)	S211R	probably benign	Het
Cab39l	T	A	14: 59,764,258 (GRCm39)	Y206*	probably null	Het
Cacna1i	A	T	15: 80,275,041 (GRCm39)	T1830S	possibly damaging	Het
Catsperg1	A	T	7: 28,889,723 (GRCm39)	L793*	probably null	Het
Cdh10	G	T	15: 18,966,108 (GRCm39)	V198F	probably damaging	Het
Cenpk	A	T	13: 104,385,917 (GRCm39)	I271F	probably damaging	Het
Chchd4	A	T	6: 91,442,260 (GRCm39)	C53S	probably damaging	Het
Cluh	T	G	11: 74,550,531 (GRCm39)	C252W	probably damaging	Het
Cmklr1	G	T	5: 113,752,710 (GRCm39)	A97E	probably damaging	Het
Coil	C	A	11: 88,871,987 (GRCm39)	A116D	possibly damaging	Het
Eif1ad9	A	G	12: 88,296,196 (GRCm39)	H58R	probably benign	Het
F830045P16Rik	C	A	2: 129,305,493 (GRCm39)	V294F	probably damaging	Het
Fgd6	T	A	10: 93,969,939 (GRCm39)	M1196K	possibly damaging	Het
Gabra5	G	A	7: 57,140,604 (GRCm39)	S31L	probably benign	Het
Gm7135	A	T	1: 97,362,790 (GRCm39)		noncoding transcript	Het
Gon4l	C	A	3: 88,794,882 (GRCm39)	T695K	probably damaging	Het
Hectd4	A	G	5: 121,491,614 (GRCm39)	H3684R	possibly damaging	Het
Ica1l	T	A	1: 60,054,917 (GRCm39)	M105L	probably benign	Het
Ift70a1	A	G	2: 75,811,147 (GRCm39)	L312P	probably damaging	Het
Igkv8-24	A	T	6: 70,194,386 (GRCm39)	V7D	probably damaging	Het
Klf10	G	A	15: 38,296,331 (GRCm39)	R420W	probably damaging	Het
Klrc2	C	A	6: 129,633,843 (GRCm39)	W177C	probably damaging	Het
Krit1	T	A	5: 3,856,451 (GRCm39)	C15*	probably null	Het
Lamc1	C	A	1: 153,103,442 (GRCm39)	V1375L	probably damaging	Het
Lrrc37a	C	T	11: 103,347,780 (GRCm39)	V2972I	unknown	Het
Mapkapk5	T	C	5: 121,672,492 (GRCm39)	D13G	probably damaging	Het
Mcph1	T	A	8: 18,838,489 (GRCm39)	L804I	probably damaging	Het
Mdn1	C	T	4: 32,723,690 (GRCm39)	P2542L	probably damaging	Het
Mrto4	A	G	4: 139,075,770 (GRCm39)	Y119H	probably benign	Het
Nbeal2	G	T	9: 110,461,158 (GRCm39)	A1635E	possibly damaging	Het
Ndufv2	A	G	17: 66,394,424 (GRCm39)	I147T	probably damaging	Het
Neb	C	A	2: 52,052,142 (GRCm39)	E382*	probably null	Het
Nhsl3	C	T	4: 129,116,478 (GRCm39)	E729K	probably damaging	Het
Nme8	T	A	13: 19,880,861 (GRCm39)	I32F	probably damaging	Het
Obox5	T	A	7: 15,491,793 (GRCm39)		probably null	Het
Or8g23	A	G	9: 38,971,065 (GRCm39)	V299A	probably benign	Het
Pcdhb19	A	T	18: 37,630,939 (GRCm39)	M245L	probably benign	Het
Pex5l	A	T	3: 33,061,477 (GRCm39)		probably null	Het
Phrf1	T	G	7: 140,840,616 (GRCm39)	D1270E	probably damaging	Het
Pik3r5	A	G	11: 68,382,790 (GRCm39)	K277E	possibly damaging	Het
Ppan	T	C	9: 20,802,221 (GRCm39)	V204A	possibly damaging	Het
Ppp1r9a	A	T	6: 5,115,367 (GRCm39)	N830I	probably damaging	Het
Pxn	C	G	5: 115,682,974 (GRCm39)	A92G	probably benign	Het
Qsox1	A	G	1: 155,666,742 (GRCm39)	V249A	probably benign	Het
Rgl3	T	A	9: 21,898,944 (GRCm39)	*88C	probably null	Het
Rps6kc1	A	T	1: 190,515,802 (GRCm39)	W975R	probably damaging	Het
Sash1	G	T	10: 8,656,368 (GRCm39)	A208D	possibly damaging	Het
Simc1	A	T	13: 54,687,709 (GRCm39)		probably benign	Het
Sox7	T	C	14: 64,185,449 (GRCm39)	Y162H	probably damaging	Het
Srp72	T	A	5: 77,128,375 (GRCm39)	L171H	probably damaging	Het
Stab1	T	A	14: 30,881,476 (GRCm39)	Y577F	probably benign	Het
Stam2	G	A	2: 52,626,305 (GRCm39)		probably benign	Het
Tagln	T	C	9: 45,842,177 (GRCm39)	T139A	probably benign	Het
Thbs3	T	C	3: 89,130,471 (GRCm39)		probably null	Het
Tmem216	G	A	19: 10,529,155 (GRCm39)	T131M	possibly damaging	Het
Tmprss11c	A	G	5: 86,404,249 (GRCm39)	V142A	probably benign	Het
Trarg1	C	G	11: 76,585,102 (GRCm39)	A164G	possibly damaging	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Ubtf	T	C	11: 102,199,128 (GRCm39)	M511V	probably null	Het
Ugt2b36	A	T	5: 87,214,114 (GRCm39)	V510E	probably damaging	Het
Vars2	G	C	17: 35,969,041 (GRCm39)	P887A	probably damaging	Het
Vmn2r80	A	G	10: 79,004,980 (GRCm39)	M206V	possibly damaging	Het
Zbtb5	A	G	4: 44,993,990 (GRCm39)	F465L	probably benign	Het
Zfp119a	G	A	17: 56,172,425 (GRCm39)	Q473*	probably null	Het
Zfp607a	T	G	7: 27,577,269 (GRCm39)	I113R	probably damaging	Het
Zfp998	A	T	13: 66,581,787 (GRCm39)	L28H	probably damaging	Het
Zmym6	C	A	4: 126,999,167 (GRCm39)	N450K	possibly damaging	Het

Other mutations in Ndc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00927:Ndc1	APN	4	107,241,977 (GRCm39)	splice site	probably benign
IGL00929:Ndc1	APN	4	107,246,694 (GRCm39)	missense	probably benign	0.23
IGL01340:Ndc1	APN	4	107,231,344 (GRCm39)	missense	probably damaging	1.00
IGL01376:Ndc1	APN	4	107,232,394 (GRCm39)	missense	probably damaging	1.00
IGL01954:Ndc1	APN	4	107,253,001 (GRCm39)	missense	probably damaging	1.00
IGL02290:Ndc1	APN	4	107,252,192 (GRCm39)	splice site	probably benign
IGL03251:Ndc1	APN	4	107,237,856 (GRCm39)	missense	possibly damaging	0.50
R1168:Ndc1	UTSW	4	107,253,009 (GRCm39)	missense	probably benign	0.02
R1541:Ndc1	UTSW	4	107,228,485 (GRCm39)	nonsense	probably null
R1605:Ndc1	UTSW	4	107,225,293 (GRCm39)	missense	probably damaging	0.96
R1612:Ndc1	UTSW	4	107,252,265 (GRCm39)	splice site	probably benign
R1716:Ndc1	UTSW	4	107,241,992 (GRCm39)	missense	probably damaging	1.00
R3522:Ndc1	UTSW	4	107,250,355 (GRCm39)	missense	probably damaging	0.99
R4036:Ndc1	UTSW	4	107,268,269 (GRCm39)	missense	probably benign	0.22
R4698:Ndc1	UTSW	4	107,268,334 (GRCm39)	missense	probably benign	0.06
R4794:Ndc1	UTSW	4	107,247,419 (GRCm39)	missense	probably benign	0.03
R5053:Ndc1	UTSW	4	107,231,415 (GRCm39)	missense	probably damaging	1.00
R5097:Ndc1	UTSW	4	107,231,358 (GRCm39)	missense	probably benign	0.01
R5158:Ndc1	UTSW	4	107,232,362 (GRCm39)	missense	probably damaging	1.00
R5579:Ndc1	UTSW	4	107,237,901 (GRCm39)	missense	possibly damaging	0.74
R5666:Ndc1	UTSW	4	107,246,723 (GRCm39)	missense	possibly damaging	0.52
R5855:Ndc1	UTSW	4	107,240,904 (GRCm39)	missense	probably damaging	1.00
R6180:Ndc1	UTSW	4	107,268,395 (GRCm39)	missense	possibly damaging	0.65
R6525:Ndc1	UTSW	4	107,225,304 (GRCm39)	missense	probably benign	0.01
R8065:Ndc1	UTSW	4	107,247,595 (GRCm39)	missense	probably benign	0.01
R8067:Ndc1	UTSW	4	107,247,595 (GRCm39)	missense	probably benign	0.01
R8100:Ndc1	UTSW	4	107,240,802 (GRCm39)	missense	possibly damaging	0.94
R8428:Ndc1	UTSW	4	107,226,017 (GRCm39)	missense	probably benign	0.00
R8952:Ndc1	UTSW	4	107,247,623 (GRCm39)	missense	probably benign	0.00
R8953:Ndc1	UTSW	4	107,238,890 (GRCm39)	missense	probably damaging	1.00
R9489:Ndc1	UTSW	4	107,247,863 (GRCm39)	critical splice donor site	probably null
R9606:Ndc1	UTSW	4	107,246,686 (GRCm39)	missense	probably damaging	0.97
Z1176:Ndc1	UTSW	4	107,243,799 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- AACTGAGAAAGTGGGTTTTCTTGC -3'
(R):5'- AGTCTACCCAGTCTGCTCTG -3'

Sequencing Primer
(F):5'- GGGTTTTCTTGCTGACTGCCC -3'
(R):5'- CTGCGTCCCTATTTTAACTACTAAC -3'

Posted On

2016-07-22