Mutagenetix > Incidental Mutation

Incidental Mutation 'R8100:Ndc1'

630444

Institutional Source

Beutler Lab

Gene Symbol

Ndc1

Ensembl Gene

ENSMUSG00000028614

Gene Name

NDC1 transmembrane nucleoporin

Synonyms

sks, 2810475A17Rik, Tmem48

MMRRC Submission

067532-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.947) question?

Stock #

R8100 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

107225244-107273543 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 107240802 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 260 (D260G)

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

possibly damaging
Transcript: ENSMUST00000139560
AA Change: D260G

PolyPhen 2 Score 0.942 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000120365
Gene: ENSMUSG00000028614
AA Change: D260G

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

Predicted Effect

probably benign
Transcript: ENSMUST00000149366
AA Change: D260G

PolyPhen 2 Score 0.430 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000137180
Gene: ENSMUSG00000028614
AA Change: D260G

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

Coding Region Coverage

1x: 99.9%
3x: 99.8%
10x: 99.4%
20x: 98.4%

Validation Efficiency

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: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adcy4	G	A	14: 56,009,722 (GRCm39)	Q777*	probably null	Het
Art1	T	C	7: 101,756,405 (GRCm39)	S199P	probably damaging	Het
Cadps2	A	T	6: 23,838,808 (GRCm39)	M110K	probably damaging	Het
Cdk13	C	T	13: 17,978,101 (GRCm39)	R379Q	unknown	Het
Cdk7	T	C	13: 100,842,925 (GRCm39)	I272V	probably benign	Het
Cep350	T	C	1: 155,829,148 (GRCm39)	D192G	probably damaging	Het
Chrna6	C	T	8: 27,903,844 (GRCm39)		probably benign	Het
Ciart	G	A	3: 95,788,656 (GRCm39)	P61L	probably damaging	Het
Ckmt1	T	A	2: 121,191,258 (GRCm39)	D223E	probably benign	Het
Col6a5	C	T	9: 105,755,839 (GRCm39)	R2195H	probably damaging	Het
D430041D05Rik	C	T	2: 104,087,287 (GRCm39)	R563H	probably benign	Het
Defa29	A	T	8: 21,816,990 (GRCm39)	M1K	probably null	Het
Dnah11	A	G	12: 117,930,368 (GRCm39)	S3326P	probably damaging	Het
Dsg3	A	G	18: 20,662,028 (GRCm39)	D431G	probably benign	Het
Ell3	TCTCCTC	TCTC	2: 121,269,937 (GRCm39)		probably benign	Het
Fbln1	T	A	15: 85,169,357 (GRCm39)	F699I	probably damaging	Het
Fndc1	A	G	17: 7,990,685 (GRCm39)	S1004P	unknown	Het
Gpr15	T	A	16: 58,538,076 (GRCm39)	T338S	probably benign	Het
Grin2d	T	C	7: 45,483,171 (GRCm39)	Y1002C	unknown	Het
Hk2	C	T	6: 82,707,859 (GRCm39)	M703I	probably benign	Het
Ifi213	A	C	1: 173,422,748 (GRCm39)	L39R	probably damaging	Het
Kctd17	CAGCTGGAGGAGC	CAGC	15: 78,321,113 (GRCm39)		probably benign	Het
Lama2	C	A	10: 26,917,113 (GRCm39)	A2271S	probably benign	Het
Lmo7	A	T	14: 102,137,899 (GRCm39)	Q867L	probably benign	Het
Loxhd1	T	A	18: 77,492,512 (GRCm39)	S1427T	possibly damaging	Het
Lzts1	A	G	8: 69,593,397 (GRCm39)	V70A	probably damaging	Het
Mocs3	A	G	2: 168,073,257 (GRCm39)	T235A	possibly damaging	Het
Myo15a	G	A	11: 60,408,016 (GRCm39)	R3168H	probably damaging	Het
Nfam1	T	C	15: 82,900,730 (GRCm39)	D44G	probably damaging	Het
Or4a47	G	A	2: 89,666,029 (GRCm39)	Q87*	probably null	Het
Osbpl10	G	A	9: 114,996,322 (GRCm39)	R128H	probably benign	Het
Otx1	C	A	11: 21,949,392 (GRCm39)	V29L	probably benign	Het
Pogk	A	T	1: 166,229,511 (GRCm39)	D113E	possibly damaging	Het
Ptgs2	T	C	1: 149,978,472 (GRCm39)	F195L	probably damaging	Het
Ptpn21	T	A	12: 98,648,881 (GRCm39)	E925V	possibly damaging	Het
Ranbp2	T	C	10: 58,326,470 (GRCm39)	F2714L	possibly damaging	Het
Rbm20	T	G	19: 53,839,744 (GRCm39)	I911S	possibly damaging	Het
Rwdd2b	A	G	16: 87,233,509 (GRCm39)	V197A	possibly damaging	Het
Sel1l2	C	G	2: 140,117,329 (GRCm39)	A181P	probably damaging	Het
Sf1	A	G	19: 6,422,368 (GRCm39)	E234G	possibly damaging	Het
Skint2	A	C	4: 112,483,197 (GRCm39)	T201P	probably damaging	Het
Sra1	C	T	18: 36,809,948 (GRCm39)	R199H	probably damaging	Het
Svs5	A	G	2: 164,079,712 (GRCm39)	M65T	probably benign	Het
Tgif1	C	A	17: 71,153,544 (GRCm39)		probably benign	Het
Tmem184c	A	G	8: 78,331,411 (GRCm39)	W113R	possibly damaging	Het
Tmem30a	T	C	9: 79,681,432 (GRCm39)	R282G	probably benign	Het
Top1	T	A	2: 160,540,155 (GRCm39)	Y244*	probably null	Het
Trank1	A	G	9: 111,221,861 (GRCm39)	Y2866C	probably damaging	Het
Trim7	A	C	11: 48,740,346 (GRCm39)	I148L	probably damaging	Het
Triml1	T	A	8: 43,591,717 (GRCm39)	M214L	probably benign	Het
Usp30	T	G	5: 114,249,245 (GRCm39)	V183G	probably damaging	Het
Vmn1r175	G	A	7: 23,508,012 (GRCm39)	S205F	probably damaging	Het
Zbtb32	CTTG	CTTGTTG	7: 30,290,946 (GRCm39)		probably benign	Het
Zfp108	T	A	7: 23,960,602 (GRCm39)	C398S	probably damaging	Het
Zfp592	T	G	7: 80,673,940 (GRCm39)	D301E	probably benign	Het
Zfp764l1	C	T	7: 126,992,496 (GRCm39)	C38Y	probably null	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
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
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'- GTAGACACTGCTCTGGTCTC -3'
(R):5'- CAATAGAGTGGCATGGCTTTGAG -3'

Sequencing Primer
(F):5'- GCTCTGGTCTCCACAGTAAG -3'
(R):5'- GAGCACAACTTTCTATACTCTGAAAC -3'

Posted On

2020-06-30