Mutagenetix > Incidental Mutation

Incidental Mutation 'R6625:Nelfe'

524764

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

044747-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6625 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

35069367-35075348 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 35073334 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 290 (P290S)

Ref Sequence

ENSEMBL: ENSMUSP00000134272 (fasta)

Gene Model

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

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

probably benign
Transcript: ENSMUST00000097343
AA Change: P290S

PolyPhen 2 Score 0.444 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000094956
Gene: ENSMUSG00000024369
AA Change: P290S

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

probably benign
Transcript: ENSMUST00000173357
AA Change: P290S

PolyPhen 2 Score 0.444 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000134272
Gene: ENSMUSG00000024369
AA Change: P290S

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: ENSMUST00000165953
AA Change: P290S

PolyPhen 2 Score 0.444 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000131195
Gene: ENSMUSG00000024369
AA Change: P290S

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

noncoding transcript
Transcript: ENSMUST00000173775

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174887

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: ENSMUST00000153400

SMART Domains

Protein: ENSMUSP00000116497
Gene: ENSMUSG00000090231

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174226

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

noncoding transcript
Transcript: ENSMUST00000174075

Predicted Effect

probably benign
Transcript: ENSMUST00000172966

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

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

noncoding transcript
Transcript: ENSMUST00000174363

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174888

Predicted Effect

probably benign
Transcript: ENSMUST00000176332

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184774

Meta Mutation Damage Score

0.1043

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.4%
20x: 91.6%

Validation Efficiency

91% (30/33)

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: 33 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akap9	C	G	5: 4,018,745 (GRCm39)	H1109D	probably benign	Het
Apcdd1	C	A	18: 63,084,929 (GRCm39)	D375E	probably damaging	Het
Cacna2d1	A	T	5: 16,567,391 (GRCm39)	R984W	probably null	Het
Csmd3	T	G	15: 47,470,471 (GRCm39)	I3402L	probably benign	Het
Dnah7a	T	A	1: 53,604,916 (GRCm39)	T1281S	probably benign	Het
Dnmt3b	T	C	2: 153,507,233 (GRCm39)	I139T	probably benign	Het
Dtnbp1	T	C	13: 45,145,507 (GRCm39)	E40G	possibly damaging	Het
Fam162b	C	T	10: 51,466,391 (GRCm39)	G43R	probably damaging	Het
G2e3	T	G	12: 51,400,572 (GRCm39)		probably null	Het
Kiss1r	G	A	10: 79,755,368 (GRCm39)	V118I	possibly damaging	Het
Mre11a	T	C	9: 14,716,687 (GRCm39)	M294T	possibly damaging	Het
Muc16	A	T	9: 18,571,574 (GRCm39)	V315D	unknown	Het
Or2v2	T	A	11: 49,003,896 (GRCm39)	Y219F	probably damaging	Het
Or5a3	T	G	19: 12,400,205 (GRCm39)	H177Q	probably damaging	Het
Pcolce2	T	A	9: 95,560,492 (GRCm39)	C180*	probably null	Het
Piezo2	A	T	18: 63,154,333 (GRCm39)	V2482D	probably damaging	Het
Plagl1	T	C	10: 13,003,806 (GRCm39)		probably benign	Het
Pramel31	T	A	4: 144,090,369 (GRCm39)	Y470N	probably damaging	Het
Pramel57	C	T	5: 95,669,342 (GRCm39)	H124Y	possibly damaging	Het
Prss48	G	T	3: 85,905,373 (GRCm39)	Q167K	probably benign	Het
Saxo4	G	A	19: 10,459,100 (GRCm39)	P65L	probably damaging	Het
Scyl1	C	A	19: 5,810,854 (GRCm39)	V488F	probably damaging	Het
Sh3pxd2b	T	A	11: 32,372,594 (GRCm39)	L587Q	possibly damaging	Het
Sim1	A	G	10: 50,860,082 (GRCm39)	D648G	probably benign	Het
Snupn	G	A	9: 56,890,054 (GRCm39)	V292I	probably benign	Het
St6galnac1	T	C	11: 116,656,717 (GRCm39)	H474R	probably damaging	Het
Thap12	G	A	7: 98,365,277 (GRCm39)	V482I	probably benign	Het
Usp13	T	A	3: 32,949,025 (GRCm39)	V454D	probably damaging	Het
Usp40	T	C	1: 87,894,935 (GRCm39)	I862V	probably benign	Het
Vmn2r59	A	T	7: 41,693,177 (GRCm39)	F474L	probably benign	Het
Zbtb38	T	C	9: 96,569,366 (GRCm39)	R573G	probably damaging	Het
Zfp493	C	T	13: 67,934,514 (GRCm39)	Q156*	probably null	Het
Zfp873	C	A	10: 81,896,138 (GRCm39)	P290T	probably 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
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
R9008:Nelfe	UTSW	17	35,073,334 (GRCm39)	missense	possibly damaging	0.90
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

2018-06-22