Mutagenetix > Incidental Mutation

Incidental Mutation 'R9008:Nelfe'

685469

Institutional Source

Beutler Lab

Gene Symbol

Nelfe

Ensembl Gene

ENSMUSG00000024369

Gene Name

negative elongation factor complex member E, Rdbp

Synonyms

NELF-E, Rdbp

MMRRC Submission

068838-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9008 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

35069367-35075348 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 35073334 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Threonine at position 290 (P290T)

Ref Sequence

ENSEMBL: ENSMUSP00000134272 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025229] [ENSMUST00000046022] [ENSMUST00000097343] [ENSMUST00000128767] [ENSMUST00000173357] [ENSMUST00000146299] [ENSMUST00000153400] [ENSMUST00000154526] [ENSMUST00000165953] [ENSMUST00000172966] [ENSMUST00000173065] [ENSMUST00000176203]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000025229

SMART Domains

Protein: ENSMUSP00000025229
Gene: ENSMUSG00000090231

Domain	Start	End	E-Value	Type
low complexity region	8	23	N/A	INTRINSIC
CCP	36	88	5.15e-1	SMART
CCP	102	157	4.62e-15	SMART
CCP	164	217	2.06e-12	SMART
VWA	267	472	1.07e-40	SMART
Tryp_SPc	480	751	2.53e-30	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000046022

SMART Domains

Protein: ENSMUSP00000036265
Gene: ENSMUSG00000040356

Domain	Start	End	E-Value	Type
low complexity region	7	22	N/A	INTRINSIC
low complexity region	171	176	N/A	INTRINSIC
low complexity region	208	237	N/A	INTRINSIC
low complexity region	269	279	N/A	INTRINSIC
DEXDc	304	487	3.61e-28	SMART
low complexity region	583	592	N/A	INTRINSIC
HELICc	619	705	8.63e-17	SMART
Pfam:rRNA_proc-arch	760	1044	9.7e-39	PFAM
DSHCT	1067	1243	7.67e-77	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000097343
AA Change: P290T

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000094956
Gene: ENSMUSG00000024369
AA Change: P290T

Domain	Start	End	E-Value	Type
coiled coil region	7	36	N/A	INTRINSIC
low complexity region	147	167	N/A	INTRINSIC
low complexity region	184	239	N/A	INTRINSIC
RRM	259	324	7.25e-12	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000128767

SMART Domains

Protein: ENSMUSP00000119977
Gene: ENSMUSG00000090231

Domain	Start	End	E-Value	Type
low complexity region	6	21	N/A	INTRINSIC
CCP	34	86	5.15e-1	SMART
CCP	100	155	4.62e-15	SMART
CCP	162	215	2.06e-12	SMART
VWA	265	470	1.07e-40	SMART
Tryp_SPc	478	749	2.53e-30	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000129891

SMART Domains

Protein: ENSMUSP00000120864
Gene: ENSMUSG00000092511

Domain	Start	End	E-Value	Type
Blast:VWA	2	77	8e-7	BLAST
Tryp_SPc	85	365	5.69e-8	SMART
CCP	310	365	4.62e-15	SMART
CCP	372	425	2.06e-12	SMART
VWA	475	680	1.07e-40	SMART
Tryp_SPc	688	959	2.53e-30	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000133127

SMART Domains

Protein: ENSMUSP00000118360
Gene: ENSMUSG00000090231

Domain	Start	End	E-Value	Type
PDB:2WIN\|L	2	43	2e-20	PDB
Blast:VWA	13	44	9e-11	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000141295

SMART Domains

Protein: ENSMUSP00000118945
Gene: ENSMUSG00000090231

Domain	Start	End	E-Value	Type
Tryp_SPc	18	258	3.76e-7	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000173357
AA Change: P290T

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000134272
Gene: ENSMUSG00000024369
AA Change: P290T

Domain	Start	End	E-Value	Type
coiled coil region	7	36	N/A	INTRINSIC
low complexity region	147	167	N/A	INTRINSIC
low complexity region	184	239	N/A	INTRINSIC
RRM	259	324	7.25e-12	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000146299

SMART Domains

Protein: ENSMUSP00000117677
Gene: ENSMUSG00000092511

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
low complexity region	72	83	N/A	INTRINSIC
CCP	94	148	1.89e-11	SMART
VWA	103	311	1.74e-1	SMART
Tryp_SPc	315	547	1.49e-7	SMART
CCP	549	601	5.15e-1	SMART
CCP	615	670	4.62e-15	SMART
CCP	677	730	2.06e-12	SMART
VWA	780	985	1.07e-40	SMART
Tryp_SPc	993	1264	2.53e-30	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000153400

SMART Domains

Protein: ENSMUSP00000116497
Gene: ENSMUSG00000090231

Domain	Start	End	E-Value	Type
Tryp_SPc	1	217	2.36e-5	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000154526

SMART Domains

Protein: ENSMUSP00000120990
Gene: ENSMUSG00000090231

Domain	Start	End	E-Value	Type
low complexity region	6	21	N/A	INTRINSIC
CCP	34	86	5.15e-1	SMART
CCP	100	155	4.62e-15	SMART
CCP	162	215	2.06e-12	SMART
VWA	265	470	1.07e-40	SMART
Tryp_SPc	478	711	5.03e-5	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000165953
AA Change: P290T

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000131195
Gene: ENSMUSG00000024369
AA Change: P290T

Domain	Start	End	E-Value	Type
coiled coil region	7	36	N/A	INTRINSIC
low complexity region	147	167	N/A	INTRINSIC
low complexity region	184	239	N/A	INTRINSIC
RRM	259	324	7.25e-12	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000172966

Predicted Effect

probably benign
Transcript: ENSMUST00000173065

SMART Domains

Protein: ENSMUSP00000133934
Gene: ENSMUSG00000024369

Domain	Start	End	E-Value	Type
coiled coil region	7	36	N/A	INTRINSIC
low complexity region	147	167	N/A	INTRINSIC
low complexity region	184	228	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000176203

SMART Domains

Protein: ENSMUSP00000135660
Gene: ENSMUSG00000090231

Domain	Start	End	E-Value	Type
low complexity region	8	23	N/A	INTRINSIC
CCP	36	88	5.15e-1	SMART
CCP	102	157	4.62e-15	SMART
CCP	164	217	2.06e-12	SMART
VWA	267	472	1.07e-40	SMART
Tryp_SPc	480	713	5.03e-5	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000176332

Meta Mutation Damage Score

0.1787

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.5%

Validation Efficiency

98% (78/80)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is part of a complex termed negative elongation factor (NELF) which represses RNA polymerase II transcript elongation. This protein bears similarity to nuclear RNA-binding proteins; however, it has not been demonstrated that this protein binds RNA. The protein contains a tract of alternating basic and acidic residues, largely arginine (R) and aspartic acid (D). The gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc4	A	T	14: 118,849,162 (GRCm39)	S536R	probably damaging	Het
Acacb	G	A	5: 114,386,815 (GRCm39)		silent	Het
Acsm1	T	C	7: 119,258,325 (GRCm39)	Y473H	probably benign	Het
Adam30	T	A	3: 98,070,034 (GRCm39)	C622*	probably null	Het
Adprs	C	T	4: 126,210,632 (GRCm39)	V283M	probably damaging	Het
AI606181	G	T	19: 41,582,032 (GRCm39)	R67S	unknown	Het
Btbd3	A	G	2: 138,125,453 (GRCm39)	I212M	probably benign	Het
C1s1	C	T	6: 124,509,499 (GRCm39)		probably null	Het
C7	T	A	15: 5,040,409 (GRCm39)	T539S		Het
Cd5l	A	C	3: 87,275,972 (GRCm39)	D314A	probably damaging	Het
Celsr3	T	A	9: 108,706,151 (GRCm39)	V878E	possibly damaging	Het
Cfap74	T	C	4: 155,503,121 (GRCm39)	S38P		Het
Chst2	C	T	9: 95,288,347 (GRCm39)		probably benign	Het
Deaf1	T	C	7: 140,904,078 (GRCm39)	T103A	probably damaging	Het
Deup1	T	A	9: 15,511,140 (GRCm39)	D213V	probably damaging	Het
Dhrs1	A	G	14: 55,978,638 (GRCm39)		probably null	Het
Dnah7a	A	G	1: 53,701,501 (GRCm39)	V218A	possibly damaging	Het
Dock7	G	A	4: 98,833,448 (GRCm39)	Q1950*	probably null	Het
Ehf	G	A	2: 103,097,173 (GRCm39)	R283W		Het
Elovl3	A	T	19: 46,123,087 (GRCm39)	N221I	possibly damaging	Het
Gm11938	A	T	11: 99,493,966 (GRCm39)	V43E	probably damaging	Het
Hmcn1	T	C	1: 150,630,795 (GRCm39)		probably benign	Het
Hnf4g	A	G	3: 3,708,096 (GRCm39)	N115S	probably benign	Het
Hnrnpr	A	T	4: 136,056,737 (GRCm39)	N246Y	probably damaging	Het
Itpka	A	G	2: 119,579,894 (GRCm39)	E211G	probably damaging	Het
Krt78	TAGGCACGGTCACCTGGCCTCCATATTCTCTCCCAGGCACGGTCACCTGGCCTCCACATTCTCCTCTAGGCACGGTCACCTGGCCTCCATATTCTCTCCCAGGCACGGTCACCTGGCCTCCAGATTCTCTTCCAGGCATGGTCACCTGGCCTCCATATTCTCTTCCAGGCACGGTCACCTGGCCTCCA	TAGGCACGGTCACCTGGCCTCCACATTCTCCTCTAGGCACGGTCACCTGGCCTCCATATTCTCTCCCAGGCACGGTCACCTGGCCTCCAGATTCTCTTCCAGGCATGGTCACCTGGCCTCCATATTCTCTTCCAGGCACGGTCACCTGGCCTCCA	15: 101,855,211 (GRCm39)		probably benign	Het
Lcorl	A	T	5: 45,931,516 (GRCm39)		probably benign	Het
Lypd9	T	A	11: 58,338,209 (GRCm39)	E61V	probably benign	Het
Mgat5	T	C	1: 127,407,308 (GRCm39)	I658T	probably damaging	Het
Mier2	G	A	10: 79,384,274 (GRCm39)	R166W	probably damaging	Het
Mov10	A	G	3: 104,707,332 (GRCm39)	Y606H	probably benign	Het
Naa38	T	G	11: 69,287,148 (GRCm39)	V76G	probably damaging	Het
Nfil3	A	T	13: 53,121,609 (GRCm39)	Y432N	probably damaging	Het
Nipbl	T	C	15: 8,356,608 (GRCm39)	K1593E	probably damaging	Het
Nlrc3	G	C	16: 3,776,807 (GRCm39)	L56V	possibly damaging	Het
Nlrp1a	A	T	11: 71,014,735 (GRCm39)	F172I	possibly damaging	Het
Ntn4	T	A	10: 93,569,466 (GRCm39)		probably benign	Het
Nudt2	G	A	4: 41,480,288 (GRCm39)	R57Q	probably damaging	Het
Obsl1	A	C	1: 75,482,027 (GRCm39)	L281W	probably benign	Het
Olfm4	A	T	14: 80,255,607 (GRCm39)	N250I	unknown	Het
Or10aa3	T	A	1: 173,878,413 (GRCm39)	V158E	probably damaging	Het
Or1x6	G	A	11: 50,938,938 (GRCm39)	M1I	probably null	Het
Or2m13	T	A	16: 19,226,173 (GRCm39)	I198F	probably benign	Het
Or2r2	T	C	6: 42,463,903 (GRCm39)	S75G	probably damaging	Het
Or5p50	A	G	7: 107,422,628 (GRCm39)	I16T	possibly damaging	Het
Pappa	A	T	4: 65,074,426 (GRCm39)	T327S	probably damaging	Het
Pcdhb4	T	G	18: 37,440,714 (GRCm39)	M8R	probably benign	Het
Phf21b	T	A	15: 84,671,563 (GRCm39)	I444F	probably damaging	Het
Pkd1l2	A	C	8: 117,769,037 (GRCm39)	V1205G	probably benign	Het
Plec	T	C	15: 76,060,232 (GRCm39)	Y3235C	probably damaging	Het
Pnmt	C	T	11: 98,278,832 (GRCm39)	T266I	possibly damaging	Het
Ppfia2	T	A	10: 106,655,220 (GRCm39)	D262E	probably benign	Het
Rabggta	A	T	14: 55,955,913 (GRCm39)	L448Q	probably damaging	Het
Rap1gds1	C	T	3: 138,661,177 (GRCm39)	R449H	probably benign	Het
Rictor	T	A	15: 6,801,610 (GRCm39)		probably benign	Het
Rttn	T	C	18: 89,027,556 (GRCm39)	F557S	probably damaging	Het
Ryr3	A	G	2: 112,465,748 (GRCm39)	C4809R	probably damaging	Het
Sacs	A	C	14: 61,441,992 (GRCm39)	D1346A	probably benign	Het
Slain1	T	A	14: 103,923,191 (GRCm39)	S261T	probably damaging	Het
Slc22a4	C	T	11: 53,881,664 (GRCm39)	W351*	probably null	Het
Smpd3	C	T	8: 106,984,058 (GRCm39)	G554S	probably benign	Het
Spag17	C	T	3: 99,934,942 (GRCm39)	S716F	possibly damaging	Het
Spata31f1e	C	T	4: 42,792,546 (GRCm39)	G529S	probably benign	Het
Spg11	C	T	2: 121,900,413 (GRCm39)	M1546I	probably benign	Het
Spmip11	T	G	15: 98,486,493 (GRCm39)	S88A	possibly damaging	Het
Stac3	C	T	10: 127,339,454 (GRCm39)	L117F	probably damaging	Het
Surf6	A	G	2: 26,782,536 (GRCm39)	W264R	probably damaging	Het
Taar7e	T	C	10: 23,913,810 (GRCm39)	V100A	probably damaging	Het
Tenm3	T	C	8: 48,795,688 (GRCm39)	H534R	probably damaging	Het
Tinagl1	C	A	4: 130,067,823 (GRCm39)	R57L	probably damaging	Het
Tnfrsf11a	G	A	1: 105,754,854 (GRCm39)	A309T	possibly damaging	Het
Traf6	A	G	2: 101,527,333 (GRCm39)	Y361C	possibly damaging	Het
Ttn	A	T	2: 76,777,334 (GRCm39)		probably benign	Het
Ufl1	A	T	4: 25,254,778 (GRCm39)	Y559*	probably null	Het
Upk1b	A	T	16: 38,607,570 (GRCm39)	N52K	probably damaging	Het
Uqcrb	A	G	13: 67,053,363 (GRCm39)	S5P	probably benign	Het
Use1	A	G	8: 71,819,688 (GRCm39)	Y3C	unknown	Het
Usp9y	T	A	Y: 1,434,993 (GRCm39)	I279L	possibly damaging	Het
Vmn1r142	A	G	7: 21,862,796 (GRCm39)	L222P	probably damaging	Het
Vmn1r184	A	C	7: 25,967,177 (GRCm39)	N308H	probably benign	Het
Vmn2r14	C	A	5: 109,367,893 (GRCm39)	M366I	probably benign	Het
Vmn2r73	G	T	7: 85,521,904 (GRCm39)	S145Y	probably damaging	Het
Wdfy1	A	T	1: 79,692,697 (GRCm39)	W207R	probably damaging	Het
Zbtb38	A	T	9: 96,569,100 (GRCm39)	N661K	probably benign	Het
Zkscan3	G	T	13: 21,572,383 (GRCm39)	H416Q	possibly damaging	Het

Other mutations in Nelfe

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00543:Nelfe	APN	17	35,072,592 (GRCm39)	missense	possibly damaging	0.81
IGL02227:Nelfe	APN	17	35,073,330 (GRCm39)	missense	probably benign	0.09
FR4342:Nelfe	UTSW	17	35,073,065 (GRCm39)	unclassified	probably benign
FR4548:Nelfe	UTSW	17	35,073,046 (GRCm39)	unclassified	probably benign
R0007:Nelfe	UTSW	17	35,072,962 (GRCm39)	unclassified	probably benign
R0563:Nelfe	UTSW	17	35,073,215 (GRCm39)	missense	possibly damaging	0.55
R2213:Nelfe	UTSW	17	35,072,859 (GRCm39)	missense	probably benign	0.03
R3802:Nelfe	UTSW	17	35,072,877 (GRCm39)	missense	possibly damaging	0.93
R5892:Nelfe	UTSW	17	35,073,645 (GRCm39)	unclassified	probably benign
R6318:Nelfe	UTSW	17	35,073,432 (GRCm39)	missense	probably damaging	1.00
R6625:Nelfe	UTSW	17	35,073,334 (GRCm39)	missense	probably benign	0.44
R6977:Nelfe	UTSW	17	35,073,688 (GRCm39)	missense	probably damaging	1.00
R7106:Nelfe	UTSW	17	35,071,395 (GRCm39)	splice site	probably null
R7205:Nelfe	UTSW	17	35,069,912 (GRCm39)	splice site	probably null
R8505:Nelfe	UTSW	17	35,073,779 (GRCm39)	splice site	probably null
RF055:Nelfe	UTSW	17	35,073,038 (GRCm39)	unclassified	probably benign
RF056:Nelfe	UTSW	17	35,073,047 (GRCm39)	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- TGAGGTGGACCCAGTAATGAC -3'
(R):5'- TCAGTCAGGAGAAAAGTTTCCTC -3'

Sequencing Primer
(F):5'- AGTAATGACTGTGGTTCCTAACCCAC -3'
(R):5'- TCAGGAGAAAAGTTTCCTCTAGAAGC -3'

Posted On

2021-10-11