Mutagenetix > Incidental Mutation

Incidental Mutation 'R1605:Ndc1'

250584

Institutional Source

Beutler Lab

Gene Symbol

Ndc1

Ensembl Gene

ENSMUSG00000028614

Gene Name

NDC1 transmembrane nucleoporin

Synonyms

sks, 2810475A17Rik, Tmem48

MMRRC Submission

039642-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.947) question?

Stock #

R1605 (G1)

Quality Score

33.8

Status

Validated

Chromosome

Chromosomal Location

107225244-107273543 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 107225293 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Lysine at position 3 (T3K)

Ref Sequence

ENSEMBL: ENSMUSP00000120365 (fasta)

Gene Model

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

AlphaFold

Q8VCB1

Predicted Effect

unknown
Transcript: ENSMUST00000030357
AA Change: T3K

Predicted Effect

unknown
Transcript: ENSMUST00000125342
AA Change: T3K

Predicted Effect

probably damaging
Transcript: ENSMUST00000139560
AA Change: T3K

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000120365
Gene: ENSMUSG00000028614
AA Change: T3K

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

Predicted Effect

probably benign
Transcript: ENSMUST00000149366
AA Change: T3K

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000137180
Gene: ENSMUSG00000028614
AA Change: T3K

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

Meta Mutation Damage Score

0.0890

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.5%
20x: 93.3%

Validation Efficiency

99% (75/76)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5730409E04Rik	A	G	4: 126,506,104 (GRCm39)	K211E	probably damaging	Het
Acot7	A	G	4: 152,291,285 (GRCm39)	I84V	possibly damaging	Het
Ankrd44	A	G	1: 54,867,781 (GRCm39)	V34A	probably benign	Het
Atp4b	A	T	8: 13,443,489 (GRCm39)	M63K	probably damaging	Het
Atr	T	A	9: 95,818,516 (GRCm39)	I2163K	probably damaging	Het
Azgp1	A	T	5: 137,983,426 (GRCm39)	R34*	probably null	Het
Ccdc152	T	G	15: 3,327,603 (GRCm39)	K58T	probably damaging	Het
Ccdc88b	T	A	19: 6,827,837 (GRCm39)	Q912L	probably benign	Het
Cdc42ep5	T	A	7: 4,154,395 (GRCm39)	H131L	probably benign	Het
Chd7	G	A	4: 8,844,675 (GRCm39)	E1595K	probably damaging	Het
Col11a1	G	A	3: 113,925,290 (GRCm39)	G41D	probably damaging	Het
Cyp2b23	C	T	7: 26,385,843 (GRCm39)	V5I	probably benign	Het
D430041D05Rik	A	G	2: 104,085,915 (GRCm39)	V22A	possibly damaging	Het
Ddi1	T	C	9: 6,266,012 (GRCm39)	Y119C	probably benign	Het
Dysf	T	C	6: 84,083,923 (GRCm39)	L785P	probably damaging	Het
Eqtn	T	A	4: 94,816,587 (GRCm39)	T69S	possibly damaging	Het
F11	T	A	8: 45,694,617 (GRCm39)	K581N	probably damaging	Het
Gli2	G	A	1: 118,782,290 (GRCm39)	P172S	probably damaging	Het
Gm7579	G	T	7: 141,765,603 (GRCm39)	C3F	unknown	Het
Grin2a	A	G	16: 9,481,194 (GRCm39)	V501A	possibly damaging	Het
Grk4	G	A	5: 34,831,901 (GRCm39)	D57N	probably damaging	Het
Gsdma	A	T	11: 98,557,319 (GRCm39)	D86V	probably damaging	Het
Gsx1	A	G	5: 147,126,738 (GRCm39)	E187G	probably damaging	Het
Hdac1-ps	A	G	17: 78,799,537 (GRCm39)	D176G	probably damaging	Het
Inpp5k	T	A	11: 75,524,307 (GRCm39)	F75L	probably benign	Het
Itpr1	T	C	6: 108,326,620 (GRCm39)	V114A	possibly damaging	Het
Izumo3	A	T	4: 92,032,977 (GRCm39)	C130S	probably damaging	Het
Mei4	G	A	9: 81,809,639 (GRCm39)	E241K	possibly damaging	Het
Mocs2	T	C	13: 114,961,120 (GRCm39)	V39A	probably benign	Het
Mroh2b	G	A	15: 4,974,572 (GRCm39)	R1184H	probably benign	Het
Msh3	T	C	13: 92,436,783 (GRCm39)	Q509R	probably null	Het
Myh8	T	C	11: 67,192,497 (GRCm39)	W1459R	probably damaging	Het
Mypop	T	A	7: 18,734,918 (GRCm39)		probably benign	Het
Nf1	A	C	11: 79,331,749 (GRCm39)	M695L	probably benign	Het
Nup50l	A	G	6: 96,141,793 (GRCm39)	M417T	probably benign	Het
Nutm2	C	A	13: 50,623,955 (GRCm39)	D217E	possibly damaging	Het
Or52a20	T	C	7: 103,365,858 (GRCm39)	I19T	probably damaging	Het
Or5b122	A	G	19: 13,562,994 (GRCm39)	T109A	probably benign	Het
Pde6c	C	A	19: 38,129,940 (GRCm39)	D283E	probably damaging	Het
Phldb2	A	G	16: 45,591,142 (GRCm39)		probably benign	Het
Pigt	G	C	2: 164,349,419 (GRCm39)	R574P	probably damaging	Het
Pkd1	T	C	17: 24,796,500 (GRCm39)	I2354T	possibly damaging	Het
Prdm15	T	C	16: 97,640,506 (GRCm39)	E27G	probably damaging	Het
Ptpn14	A	G	1: 189,597,709 (GRCm39)	I1140V	probably benign	Het
Rdx	T	C	9: 51,974,891 (GRCm39)	V9A	probably damaging	Het
Rfx7	T	C	9: 72,519,071 (GRCm39)	S258P	probably damaging	Het
Rnf17	G	T	14: 56,730,822 (GRCm39)	G1209C	probably damaging	Het
S1pr4	C	T	10: 81,335,225 (GRCm39)		probably null	Het
Scml2	G	T	X: 160,014,442 (GRCm39)	E566D	possibly damaging	Het
Serpinb1b	T	A	13: 33,277,646 (GRCm39)	V293E	possibly damaging	Het
Serpinb9b	T	C	13: 33,222,112 (GRCm39)		probably null	Het
Sez6l	A	C	5: 112,622,915 (GRCm39)	I212S	probably damaging	Het
Son	T	C	16: 91,454,552 (GRCm39)	S1100P	probably damaging	Het
Spag9	G	A	11: 93,939,365 (GRCm39)	R98H	probably damaging	Het
Spata31e2	A	T	1: 26,723,511 (GRCm39)	H556Q	possibly damaging	Het
St3gal5	T	C	6: 72,119,272 (GRCm39)	L128P	probably benign	Het
Stra6	A	T	9: 58,059,166 (GRCm39)	M510L	probably benign	Het
Stxbp5l	A	G	16: 37,028,473 (GRCm39)	V530A	probably benign	Het
Tatdn1	A	G	15: 58,793,039 (GRCm39)		probably benign	Het
Tbc1d8	A	G	1: 39,430,206 (GRCm39)	S466P	probably benign	Het
Tmem199	A	T	11: 78,399,152 (GRCm39)	M175K	possibly damaging	Het
Trmt12	A	G	15: 58,744,764 (GRCm39)	E54G	probably benign	Het
Usp37	G	T	1: 74,532,163 (GRCm39)	Q77K	possibly damaging	Het
Vezf1	A	G	11: 87,967,125 (GRCm39)	I301V	possibly damaging	Het
Vmn1r34	T	G	6: 66,613,932 (GRCm39)	M269L	probably benign	Het
Wdr93	C	A	7: 79,421,257 (GRCm39)		probably null	Het
Wnk2	T	C	13: 49,214,370 (GRCm39)	D644G	probably damaging	Het
Zc3h13	C	T	14: 75,574,923 (GRCm39)	R1591*	probably null	Het
Zfp131	G	A	13: 120,230,316 (GRCm39)	L371F	probably damaging	Het
Zfp180	T	A	7: 23,804,049 (GRCm39)	V156D	probably benign	Het
Zfp646	G	T	7: 127,479,359 (GRCm39)		probably null	Het
Zscan12	C	A	13: 21,550,813 (GRCm39)	T144K	probably benign	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
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
R5217:Ndc1	UTSW	4	107,246,773 (GRCm39)	missense	probably benign
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'- AGTTCCAGAATGCAACGCTCCTC -3'
(R):5'- ACGCTATTCCTAAAGCGCCTCCAAG -3'

Sequencing Primer
(F):5'- TTTTGACGCCCAGATGGAC -3'
(R):5'- TCCAAGACAGGCCCCTTTAG -3'

Posted On

2014-11-14