Mutagenetix > Incidental Mutation

Incidental Mutation 'R1533:Nelfa'

166730

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

039572-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1533 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

34055263-34093615 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 34056215 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamine at position 483 (K483Q)

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: K483Q

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000030993
Gene: ENSMUSG00000029111
AA Change: K483Q

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

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 92.9%

Validation Efficiency

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca4	G	C	3: 121,928,807 (GRCm39)	G1340A	probably benign	Het
Ambra1	T	A	2: 91,717,210 (GRCm39)	Y836N	probably damaging	Het
Arhgap26	A	T	18: 39,504,130 (GRCm39)	H144L	probably benign	Het
B3gnt5	A	G	16: 19,588,364 (GRCm39)	I194M	probably damaging	Het
Bltp1	G	T	3: 37,095,524 (GRCm39)	G4509V	probably damaging	Het
Bod1l	A	T	5: 41,979,498 (GRCm39)	C605*	probably null	Het
C2cd3	G	T	7: 100,055,284 (GRCm39)	K482N	possibly damaging	Het
Cd300lg	T	A	11: 101,934,047 (GRCm39)	L98Q	probably damaging	Het
Cerkl	T	A	2: 79,171,701 (GRCm39)	I386F	possibly damaging	Het
Cfh	T	A	1: 140,028,716 (GRCm39)	D466V	possibly damaging	Het
Crtc1	A	T	8: 70,850,949 (GRCm39)	I221N	probably damaging	Het
Ctnnbl1	T	C	2: 157,678,563 (GRCm39)	S389P	probably benign	Het
Ctsb	A	T	14: 63,376,544 (GRCm39)	D258V	probably damaging	Het
Cuzd1	G	T	7: 130,913,432 (GRCm39)	T395N	probably damaging	Het
Dnah6	T	C	6: 73,128,536 (GRCm39)	T1240A	probably benign	Het
Dok7	T	A	5: 35,221,671 (GRCm39)		probably null	Het
Dscaml1	T	C	9: 45,361,882 (GRCm39)	V214A	probably damaging	Het
Enpp6	A	T	8: 47,518,469 (GRCm39)	Y199F	probably benign	Het
Entpd5	C	A	12: 84,441,434 (GRCm39)	K111N	probably damaging	Het
Fam98a	A	G	17: 75,848,276 (GRCm39)	L146S	probably damaging	Het
Fhod3	A	T	18: 25,248,921 (GRCm39)	I1367F	probably damaging	Het
Fmnl2	A	G	2: 52,995,549 (GRCm39)	E424G	probably damaging	Het
Fpr3	T	A	17: 18,190,922 (GRCm39)	Y64*	probably null	Het
Fzd6	A	T	15: 38,895,019 (GRCm39)	H395L	probably damaging	Het
Gcsh	T	A	8: 117,715,921 (GRCm39)	H54L	probably damaging	Het
Gsdma	T	A	11: 98,567,210 (GRCm39)	S437T	unknown	Het
Gzmc	A	G	14: 56,471,376 (GRCm39)	V55A	probably damaging	Het
Hecw2	T	A	1: 53,965,704 (GRCm39)		probably null	Het
Ifi207	A	G	1: 173,555,306 (GRCm39)	V792A	probably benign	Het
Itpr3	C	A	17: 27,314,534 (GRCm39)	N661K	possibly damaging	Het
Jmy	A	T	13: 93,577,819 (GRCm39)	I783N	probably benign	Het
Kcmf1	T	C	6: 72,820,003 (GRCm39)	E281G	possibly damaging	Het
Klra3	G	C	6: 130,310,107 (GRCm39)	R138G	probably benign	Het
Lgr6	T	A	1: 135,032,670 (GRCm39)	Y70F	possibly damaging	Het
Lnx1	T	G	5: 74,780,678 (GRCm39)	D330A	probably damaging	Het
Lrp5	T	C	19: 3,664,234 (GRCm39)	N106S	probably benign	Het
Mamdc4	C	A	2: 25,459,759 (GRCm39)	R135L	possibly damaging	Het
Mcm3ap	A	G	10: 76,340,121 (GRCm39)	E1464G	probably damaging	Het
Megf8	T	C	7: 25,034,280 (GRCm39)	V666A	possibly damaging	Het
Mettl3	T	A	14: 52,534,385 (GRCm39)	E331D	probably benign	Het
Mphosph9	T	C	5: 124,405,204 (GRCm39)	K789R	probably damaging	Het
Mtf2	T	C	5: 108,239,995 (GRCm39)	L234P	probably damaging	Het
Ncdn	C	A	4: 126,642,491 (GRCm39)	E389*	probably null	Het
Ndor1	A	G	2: 25,139,279 (GRCm39)	S231P	probably damaging	Het
Odad1	T	A	7: 45,592,282 (GRCm39)	M354K	probably benign	Het
Opn1sw	C	T	6: 29,378,923 (GRCm39)	R243Q	probably benign	Het
Or13a24	T	A	7: 140,155,034 (GRCm39)		probably null	Het
Or9e1	A	G	11: 58,732,792 (GRCm39)	N284S	probably damaging	Het
Pik3cd	T	C	4: 149,739,653 (GRCm39)	E584G	probably damaging	Het
Plcb3	A	T	19: 6,935,041 (GRCm39)	M870K	possibly damaging	Het
Poc5	A	G	13: 96,528,152 (GRCm39)	D16G	probably damaging	Het
Prpf40a	A	G	2: 53,035,852 (GRCm39)	I633T	probably damaging	Het
Ptpn13	G	T	5: 103,704,044 (GRCm39)	E1359*	probably null	Het
Ptprr	C	A	10: 116,024,113 (GRCm39)	Y4*	probably null	Het
Rbm45	T	C	2: 76,202,503 (GRCm39)		probably null	Het
Rfng	C	T	11: 120,672,687 (GRCm39)	W320*	probably null	Het
Rgs6	G	T	12: 83,138,547 (GRCm39)	V294L	probably benign	Het
Rufy4	T	C	1: 74,169,002 (GRCm39)		probably null	Het
Ruvbl2	T	A	7: 45,073,566 (GRCm39)	N313I	probably damaging	Het
Sema4g	G	A	19: 44,981,256 (GRCm39)	V70M	probably damaging	Het
Siglec1	T	C	2: 130,918,078 (GRCm39)	T969A	probably benign	Het
Slc22a27	T	A	19: 7,844,348 (GRCm39)	T431S	possibly damaging	Het
Slc25a16	G	A	10: 62,756,643 (GRCm39)	R38H	probably damaging	Het
Slc38a6	T	C	12: 73,391,626 (GRCm39)	V296A	probably benign	Het
Slc39a11	C	T	11: 113,196,748 (GRCm39)	V212I	probably damaging	Het
Sltm	A	G	9: 70,493,948 (GRCm39)	K782E	probably damaging	Het
Styxl1	T	A	5: 135,799,175 (GRCm39)	Y23F	probably damaging	Het
Svs4	T	C	2: 164,120,148 (GRCm39)	I20V	unknown	Het
Syt14	G	T	1: 192,613,084 (GRCm39)	T572K	possibly damaging	Het
Tbc1d5	A	T	17: 51,227,603 (GRCm39)	I214N	possibly damaging	Het
Tm9sf3	A	G	19: 41,227,223 (GRCm39)	S283P	probably benign	Het
Tmtc1	C	T	6: 148,147,208 (GRCm39)		probably null	Het
Ttll7	T	A	3: 146,602,422 (GRCm39)	N73K	probably damaging	Het
Ttn	T	A	2: 76,602,802 (GRCm39)	K18473N	probably damaging	Het
Ubr2	A	C	17: 47,278,173 (GRCm39)	Y721*	probably null	Het
Vmn1r14	T	A	6: 57,211,286 (GRCm39)	I288N	probably damaging	Het
Vmn2r103	T	C	17: 19,993,662 (GRCm39)	I13T	probably benign	Het
Vps13a	A	T	19: 16,678,494 (GRCm39)	Y1162*	probably null	Het
Vps51	C	A	19: 6,121,497 (GRCm39)	R175L	probably benign	Het
Zfp523	C	A	17: 28,423,473 (GRCm39)	S149R	probably benign	Het
Zik1	A	G	7: 10,224,053 (GRCm39)	I348T	possibly damaging	Het
Znfx1	T	A	2: 166,898,708 (GRCm39)	H72L	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
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
R6153:Nelfa	UTSW	5	34,056,223 (GRCm39)	missense	probably damaging	1.00
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'- TGCTCAGGTCACTCAGCACAAC -3'
(R):5'- AGACGGCAAACAAGGTCACTCG -3'

Sequencing Primer
(F):5'- AGCAAACCTTGTCCTCTGG -3'
(R):5'- GGAGAAGGCCCTCATCCTG -3'

Posted On

2014-04-13