Mutagenetix > Incidental Mutation

Incidental Mutation 'R6153:Nelfa'

489375

Institutional Source

Beutler Lab

Gene Symbol

Nelfa

Ensembl Gene

ENSMUSG00000029111

Gene Name

negative elongation factor complex member A, Whsc2

Synonyms

Whsc2h, Nelf-A, Whsc2

MMRRC Submission

044300-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6153 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

34055263-34093615 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 34056223 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 480 (I480N)

Ref Sequence

ENSEMBL: ENSMUSP00000030993 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030993] [ENSMUST00000058096] [ENSMUST00000066854] [ENSMUST00000075812] [ENSMUST00000137191] [ENSMUST00000139845] [ENSMUST00000202525]

AlphaFold

Q8BG30

Predicted Effect

probably damaging
Transcript: ENSMUST00000030993
AA Change: I480N

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000030993
Gene: ENSMUSG00000029111
AA Change: I480N

Domain	Start	End	E-Value	Type
low complexity region	54	63	N/A	INTRINSIC
low complexity region	280	294	N/A	INTRINSIC
low complexity region	315	333	N/A	INTRINSIC
low complexity region	339	365	N/A	INTRINSIC
low complexity region	383	429	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000058096

SMART Domains

Protein: ENSMUSP00000058940
Gene: ENSMUSG00000057406

Domain	Start	End	E-Value	Type
low complexity region	12	23	N/A	INTRINSIC
PWWP	220	285	3.84e-15	SMART
low complexity region	397	408	N/A	INTRINSIC
HMG	452	522	7.64e-9	SMART
low complexity region	532	545	N/A	INTRINSIC
low complexity region	629	643	N/A	INTRINSIC
PHD	669	711	1.36e-6	SMART
RING	670	710	1.5e1	SMART
PHD	716	763	6.81e-1	SMART
RING	717	762	5.25e-2	SMART
PHD	833	873	2.35e-10	SMART
PWWP	878	940	2.67e-23	SMART
AWS	1011	1062	3.74e-27	SMART
SET	1063	1186	4.48e-43	SMART
PostSET	1187	1203	7.56e-4	SMART
low complexity region	1215	1236	N/A	INTRINSIC
PHD	1241	1284	1.98e-8	SMART
low complexity region	1347	1360	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000066854

SMART Domains

Protein: ENSMUSP00000067205
Gene: ENSMUSG00000057406

Domain	Start	End	E-Value	Type
low complexity region	12	23	N/A	INTRINSIC
PWWP	220	285	3.84e-15	SMART
low complexity region	397	408	N/A	INTRINSIC
HMG	452	522	7.64e-9	SMART
low complexity region	532	545	N/A	INTRINSIC
low complexity region	630	644	N/A	INTRINSIC
PHD	670	712	1.36e-6	SMART
RING	671	711	1.5e1	SMART
PHD	717	764	6.81e-1	SMART
RING	718	763	5.25e-2	SMART
PHD	834	874	2.35e-10	SMART
PWWP	879	941	2.67e-23	SMART
AWS	1012	1063	3.74e-27	SMART
SET	1064	1187	4.48e-43	SMART
PostSET	1188	1204	7.56e-4	SMART
low complexity region	1216	1237	N/A	INTRINSIC
PHD	1242	1285	1.98e-8	SMART
low complexity region	1348	1361	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000075812

SMART Domains

Protein: ENSMUSP00000075210
Gene: ENSMUSG00000057406

Domain	Start	End	E-Value	Type
low complexity region	12	23	N/A	INTRINSIC
PWWP	220	285	3.84e-15	SMART
low complexity region	397	408	N/A	INTRINSIC
HMG	452	522	7.64e-9	SMART
low complexity region	532	545	N/A	INTRINSIC
low complexity region	630	644	N/A	INTRINSIC
PHD	670	712	1.36e-6	SMART
RING	671	711	1.5e1	SMART
PHD	717	764	6.81e-1	SMART
RING	718	763	5.25e-2	SMART
PHD	834	874	2.35e-10	SMART
PWWP	879	941	2.67e-23	SMART
AWS	1012	1063	3.74e-27	SMART
SET	1064	1187	4.48e-43	SMART
PostSET	1188	1204	7.56e-4	SMART
low complexity region	1216	1237	N/A	INTRINSIC
PHD	1242	1285	1.98e-8	SMART
low complexity region	1348	1361	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000137191

SMART Domains

Protein: ENSMUSP00000122310
Gene: ENSMUSG00000057406

Domain	Start	End	E-Value	Type
low complexity region	12	23	N/A	INTRINSIC
Pfam:PWWP	220	332	4.9e-26	PFAM
low complexity region	397	408	N/A	INTRINSIC
HMG	452	522	7.64e-9	SMART
low complexity region	532	545	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000139845

SMART Domains

Protein: ENSMUSP00000123460
Gene: ENSMUSG00000057406

Domain	Start	End	E-Value	Type
low complexity region	12	23	N/A	INTRINSIC
Pfam:PWWP	220	332	4.9e-26	PFAM
low complexity region	397	408	N/A	INTRINSIC
HMG	452	522	7.64e-9	SMART
low complexity region	532	545	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000141416

SMART Domains

Protein: ENSMUSP00000117233
Gene: ENSMUSG00000057406

Domain	Start	End	E-Value	Type
Pfam:PWWP	202	314	1.1e-25	PFAM
low complexity region	379	390	N/A	INTRINSIC
HMG	434	504	4.7e-9	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183676

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201572

Predicted Effect

probably benign
Transcript: ENSMUST00000202525

SMART Domains

Protein: ENSMUSP00000144255
Gene: ENSMUSG00000057406

Domain	Start	End	E-Value	Type
PHD	11	53	8.5e-9	SMART
RING	12	52	7.3e-2	SMART
PHD	58	105	4.4e-3	SMART
RING	59	104	2.6e-4	SMART
PHD	175	215	1.5e-12	SMART
low complexity region	248	259	N/A	INTRINSIC

Meta Mutation Damage Score

0.6338

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.0%
20x: 94.3%

Validation Efficiency

99% (66/67)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is expressed ubiquitously with higher levels in fetal than in adult tissues. It encodes a protein sharing 93% sequence identity with the mouse protein. Wolf-Hirschhorn syndrome (WHS) is a malformation syndrome associated with a hemizygous deletion of the distal short arm of chromosome 4. This gene is mapped to the 165 kb WHS critical region, and may play a role in the phenotype of the WHS or Pitt-Rogers-Danks syndrome. The encoded protein is found to be capable of reacting with HLA-A2-restricted and tumor-specific cytotoxic T lymphocytes, suggesting a target for use in specific immunotherapy for a large number of cancer patients. This protein has also been shown to be a member of the NELF (negative elongation factor) protein complex that participates in the regulation of RNA polymerase II transcription elongation. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	G	T	11: 9,251,259 (GRCm39)		probably null	Het
Ache	T	C	5: 137,290,117 (GRCm39)	I394T	probably damaging	Het
Acsm1	G	A	7: 119,232,289 (GRCm39)	G62D	probably damaging	Het
Actrt3	T	A	3: 30,653,899 (GRCm39)	I34F	probably damaging	Het
Adgrf5	T	C	17: 43,761,974 (GRCm39)	I1223T	possibly damaging	Het
Adora2a	T	C	10: 75,161,981 (GRCm39)	F40S	possibly damaging	Het
Ano8	T	C	8: 71,933,441 (GRCm39)		probably benign	Het
Arid1b	T	A	17: 5,293,107 (GRCm39)	L675Q	probably damaging	Het
Atg2b	T	C	12: 105,589,741 (GRCm39)	I1837V	possibly damaging	Het
Atp10b	A	G	11: 43,145,109 (GRCm39)	Y1284C	probably damaging	Het
B3gnt7	G	T	1: 86,233,237 (GRCm39)	G44V	probably damaging	Het
Chrna1	G	T	2: 73,403,653 (GRCm39)	H99N	probably benign	Het
Cnksr1	T	C	4: 133,961,204 (GRCm39)	H220R	probably damaging	Het
Cpsf2	T	A	12: 101,965,619 (GRCm39)		probably null	Het
Daglb	T	C	5: 143,489,096 (GRCm39)	L651P	probably benign	Het
Ddx60	A	G	8: 62,398,974 (GRCm39)	D231G	possibly damaging	Het
Ehd4	A	C	2: 119,932,904 (GRCm39)	F174C	probably damaging	Het
Emsy	G	T	7: 98,260,060 (GRCm39)	P9T	probably damaging	Het
Fnbp1l	T	C	3: 122,352,805 (GRCm39)	E217G	probably benign	Het
Gm11596	A	T	11: 99,683,524 (GRCm39)	C199S	unknown	Het
Gmps	T	G	3: 63,908,964 (GRCm39)	C489G	probably benign	Het
Gpsm1	T	C	2: 26,215,425 (GRCm39)	Y296H	probably benign	Het
Heatr5b	T	C	17: 79,138,870 (GRCm39)	T91A	possibly damaging	Het
Hs3st3b1	A	T	11: 63,780,324 (GRCm39)	W268R	probably damaging	Het
Il27ra	T	C	8: 84,758,773 (GRCm39)		probably null	Het
Itga5	T	A	15: 103,265,880 (GRCm39)	I156F	probably damaging	Het
Kcnmb3	T	A	3: 32,527,976 (GRCm39)	D96V	probably damaging	Het
Khdrbs1	T	A	4: 129,609,965 (GRCm39)	N417Y	probably damaging	Het
Loxhd1	A	G	18: 77,383,454 (GRCm39)	N118D	possibly damaging	Het
Mdm4	A	G	1: 132,919,845 (GRCm39)	L341P	probably damaging	Het
Mecom	T	C	3: 30,047,797 (GRCm39)	E225G	possibly damaging	Het
Megf8	G	A	7: 25,046,796 (GRCm39)	G1560S	possibly damaging	Het
Mfsd13a	A	T	19: 46,356,321 (GRCm39)	D142V	probably damaging	Het
Muc5b	A	T	7: 141,415,181 (GRCm39)	Y2709F	possibly damaging	Het
Or10ak8	G	A	4: 118,773,944 (GRCm39)	S240F	probably damaging	Het
Or8b36	ATTGCTGTTT	ATTGCTGTTTGCTGTTT	9: 37,937,836 (GRCm39)		probably null	Het
Palld	G	T	8: 62,003,186 (GRCm39)	N304K	probably damaging	Het
Pcsk5	A	G	19: 17,488,856 (GRCm39)	L988P	probably damaging	Het
Prmt1	A	T	7: 44,631,251 (GRCm39)	F34I	probably damaging	Het
Pzp	A	G	6: 128,465,979 (GRCm39)	S1234P	probably benign	Het
Ralb	A	T	1: 119,405,870 (GRCm39)		probably null	Het
Robo2	T	A	16: 73,717,617 (GRCm39)	D141V	probably damaging	Het
Rsrc1	T	C	3: 67,262,895 (GRCm39)	I283T	probably benign	Het
Sec62	A	T	3: 30,864,631 (GRCm39)	K165M	unknown	Het
Sez6	A	G	11: 77,868,648 (GRCm39)	D974G	probably damaging	Het
Shc2	T	A	10: 79,465,752 (GRCm39)	I187F	possibly damaging	Het
Shroom3	G	A	5: 93,112,267 (GRCm39)	R1876Q	probably damaging	Het
Siglecg	C	A	7: 43,061,441 (GRCm39)	N481K	possibly damaging	Het
Skil	T	A	3: 31,152,002 (GRCm39)	F175I	probably damaging	Het
Slc1a1	T	C	19: 28,886,935 (GRCm39)	V432A	probably damaging	Het
Slit3	G	T	11: 35,591,310 (GRCm39)	G1374V	possibly damaging	Het
Snx14	T	C	9: 88,273,859 (GRCm39)	Y644C	probably damaging	Het
Snx33	T	A	9: 56,833,983 (GRCm39)	I29F	possibly damaging	Het
Sos1	T	A	17: 80,756,764 (GRCm39)	I263L	probably benign	Het
Susd2	C	T	10: 75,473,853 (GRCm39)	A581T	probably damaging	Het
Tbpl2	C	A	2: 23,966,028 (GRCm39)	V320F	probably damaging	Het
Tmem209	A	G	6: 30,505,794 (GRCm39)	S171P	probably benign	Het
Tprkb	T	A	6: 85,893,172 (GRCm39)		probably null	Het
Tspan11	G	A	6: 127,916,061 (GRCm39)	S119N	probably benign	Het
Ulk2	A	T	11: 61,672,572 (GRCm39)	V922D	probably damaging	Het
Zfp267	A	G	3: 36,219,303 (GRCm39)	H442R	possibly damaging	Het
Zfp976	A	C	7: 42,263,610 (GRCm39)	Y76D	probably damaging	Het
Zkscan2	G	A	7: 123,088,993 (GRCm39)	T426I	probably benign	Het

Other mutations in Nelfa

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01448:Nelfa	APN	5	34,056,146 (GRCm39)	missense	probably damaging	0.98
R0590:Nelfa	UTSW	5	34,059,169 (GRCm39)	missense	probably damaging	1.00
R0613:Nelfa	UTSW	5	34,060,807 (GRCm39)	splice site	probably benign
R1533:Nelfa	UTSW	5	34,056,215 (GRCm39)	missense	probably damaging	0.98
R2181:Nelfa	UTSW	5	34,057,853 (GRCm39)	missense	probably benign	0.43
R4246:Nelfa	UTSW	5	34,056,373 (GRCm39)	missense	probably damaging	1.00
R4398:Nelfa	UTSW	5	34,058,623 (GRCm39)	missense	possibly damaging	0.66
R4657:Nelfa	UTSW	5	34,059,157 (GRCm39)	missense	probably benign	0.08
R4973:Nelfa	UTSW	5	34,059,162 (GRCm39)	missense	probably benign	0.04
R5424:Nelfa	UTSW	5	34,079,189 (GRCm39)	critical splice donor site	probably null
R5614:Nelfa	UTSW	5	34,077,844 (GRCm39)	missense	probably damaging	1.00
R5737:Nelfa	UTSW	5	34,056,457 (GRCm39)	critical splice acceptor site	probably null
R6135:Nelfa	UTSW	5	34,056,620 (GRCm39)	splice site	probably null
R7231:Nelfa	UTSW	5	34,056,169 (GRCm39)	missense	probably damaging	1.00
R8168:Nelfa	UTSW	5	34,079,251 (GRCm39)	missense	possibly damaging	0.88
R8175:Nelfa	UTSW	5	34,079,357 (GRCm39)	missense	possibly damaging	0.86
R8446:Nelfa	UTSW	5	34,058,982 (GRCm39)	missense	probably damaging	0.99
R8971:Nelfa	UTSW	5	34,093,539 (GRCm39)	missense	possibly damaging	0.92
R9474:Nelfa	UTSW	5	34,056,095 (GRCm39)	missense	probably damaging	1.00
R9616:Nelfa	UTSW	5	34,059,127 (GRCm39)	missense	possibly damaging	0.66

Predicted Primers

PCR Primer
(F):5'- GCAGAGATGGCACTTAGGAC -3'
(R):5'- AGAGAACAGATGTTTGCTGCC -3'

Sequencing Primer
(F):5'- CACTTAGGACACATTGGTCATAGGC -3'
(R):5'- CTGCCCAGGAGATGTTCAAGAC -3'

Posted On

2017-10-10