Mutagenetix > Incidental Mutation

Incidental Mutation 'R7231:Nelfa'

562455

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

045342-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7231 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

34055263-34093615 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 34056169 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Aspartic acid at position 498 (G498D)

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: G498D

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000030993
Gene: ENSMUSG00000029111
AA Change: G498D

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

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

0.0719

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

98% (78/80)

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
Abca13	A	T	11: 9,244,175 (GRCm39)	T2013S	probably benign	Het
Ablim3	A	G	18: 61,938,135 (GRCm39)		probably null	Het
Acvrl1	T	A	15: 101,034,104 (GRCm39)	C206*	probably null	Het
Adamts15	C	A	9: 30,817,454 (GRCm39)	R541S	probably damaging	Het
Add3	A	G	19: 53,221,577 (GRCm39)	I230V	probably benign	Het
Ankrd27	A	G	7: 35,327,871 (GRCm39)	D742G	possibly damaging	Het
Asxl3	A	G	18: 22,650,597 (GRCm39)	E862G	probably damaging	Het
Asxl3	A	T	18: 22,544,556 (GRCm39)		probably null	Het
Atp2b2	G	A	6: 113,742,693 (GRCm39)	T798M	possibly damaging	Het
Car12	T	C	9: 66,659,599 (GRCm39)	I208T	probably damaging	Het
Cgn	T	A	3: 94,680,502 (GRCm39)	Q600L	probably damaging	Het
Cgnl1	C	T	9: 71,539,927 (GRCm39)	A1106T	probably benign	Het
Cmtr2	T	C	8: 110,949,178 (GRCm39)	V496A	probably benign	Het
Cplx4	C	A	18: 66,090,123 (GRCm39)	D99Y	probably damaging	Het
Cyfip2	T	C	11: 46,114,963 (GRCm39)	T915A	probably benign	Het
Cyp4a32	T	C	4: 115,466,894 (GRCm39)	L193P	probably damaging	Het
Dennd5b	C	T	6: 148,946,102 (GRCm39)	R503Q	probably damaging	Het
Depdc5	C	A	5: 33,059,209 (GRCm39)	Q303K	possibly damaging	Het
Dlx1	T	A	2: 71,362,840 (GRCm39)	M249K	possibly damaging	Het
Dnah10	A	T	5: 124,890,892 (GRCm39)	E3218V	probably benign	Het
Dnah9	T	C	11: 65,856,473 (GRCm39)	D2896G	probably damaging	Het
Dtx4	C	A	19: 12,447,022 (GRCm39)	G557*	probably null	Het
Eps8l2	A	G	7: 140,940,305 (GRCm39)	N512D	probably damaging	Het
Fam20a	T	C	11: 109,612,201 (GRCm39)	D114G	possibly damaging	Het
Fbln1	T	C	15: 85,090,353 (GRCm39)	S7P	unknown	Het
Fli1	T	C	9: 32,335,484 (GRCm39)	E316G	probably damaging	Het
Fmn2	CCCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATATCTCCCCTACCTCCTCTCCCTGGAATGGGAATACCTCC	CCCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATATCTCCCCTACCTCCTCTCCCTGGAATGGGAATACCTCC	1: 174,436,769 (GRCm39)		probably benign	Het
Haus8	G	A	8: 71,705,781 (GRCm39)	T302I	probably benign	Het
Hmcn1	T	C	1: 150,514,627 (GRCm39)	I3582V	probably benign	Het
Hnrnpul1	G	A	7: 25,447,842 (GRCm39)	Q161*	probably null	Het
Hsf4	C	T	8: 105,998,779 (GRCm39)	A223V	probably damaging	Het
Ighg2c	A	G	12: 113,251,636 (GRCm39)	W164R		Het
Isl1	A	G	13: 116,439,826 (GRCm39)	V174A	probably benign	Het
Itih4	A	T	14: 30,618,571 (GRCm39)	I661F	probably benign	Het
Klhl14	A	T	18: 21,785,193 (GRCm39)	L78Q	probably damaging	Het
L3mbtl3	T	A	10: 26,215,180 (GRCm39)	I177F	unknown	Het
Lingo3	T	A	10: 80,670,938 (GRCm39)	T331S	possibly damaging	Het
Lrrc36	T	C	8: 106,187,689 (GRCm39)	V535A	possibly damaging	Het
Mapk8ip2	T	G	15: 89,342,279 (GRCm39)	S497A	probably benign	Het
Mbip	A	G	12: 56,384,547 (GRCm39)		probably null	Het
Nherf2	C	T	17: 24,869,078 (GRCm39)	R16H	probably damaging	Het
Nlrc5	T	A	8: 95,248,433 (GRCm39)		probably null	Het
Or2ag2b	A	T	7: 106,417,650 (GRCm39)	Y120F	probably damaging	Het
Or4f59	A	T	2: 111,872,711 (GRCm39)	V222D	probably damaging	Het
Or56a3	T	C	7: 104,734,994 (GRCm39)	S24P	possibly damaging	Het
Or7e171-ps1	T	A	9: 19,852,855 (GRCm39)	T294S	unknown	Het
Pde2a	A	G	7: 101,155,160 (GRCm39)	Y567C	probably damaging	Het
Pdia4	A	T	6: 47,777,891 (GRCm39)	F367Y	probably benign	Het
Pkdrej	C	A	15: 85,700,389 (GRCm39)	C1849F	possibly damaging	Het
Plekhj1	T	G	10: 80,633,492 (GRCm39)	T52P	probably damaging	Het
Ppp2r5d	A	T	17: 46,994,986 (GRCm39)	Y572N	probably benign	Het
Prkcq	T	A	2: 11,295,262 (GRCm39)	Y570*	probably null	Het
Ptpn3	T	A	4: 57,245,062 (GRCm39)	D226V	probably damaging	Het
Rab1b	A	G	19: 5,155,229 (GRCm39)	S22P	probably damaging	Het
Ralgapa1	A	G	12: 55,650,976 (GRCm39)	S2060P	probably damaging	Het
Rnf148	G	T	6: 23,654,890 (GRCm39)	S35R	probably benign	Het
Runx2	G	A	17: 45,125,079 (GRCm39)	P80L	probably damaging	Het
Samd15	T	A	12: 87,247,818 (GRCm39)	S168T	possibly damaging	Het
Slc26a4	T	A	12: 31,597,945 (GRCm39)	N167I	probably damaging	Het
Slc39a1	C	A	3: 90,159,097 (GRCm39)	H141Q	probably benign	Het
Snx21	T	C	2: 164,628,121 (GRCm39)	S46P	probably benign	Het
Strip2	A	G	6: 29,944,486 (GRCm39)	S657G	probably damaging	Het
Stxbp3	G	A	3: 108,708,125 (GRCm39)	P392L	probably damaging	Het
Suclg1	G	A	6: 73,240,954 (GRCm39)	R161H	probably benign	Het
Tas1r3	T	C	4: 155,947,283 (GRCm39)	Y134C	probably damaging	Het
Tgif1	T	A	17: 71,153,168 (GRCm39)	Q114L	probably damaging	Het
Tll2	A	G	19: 41,074,673 (GRCm39)	F964L	probably benign	Het
Tmem181a	T	C	17: 6,348,195 (GRCm39)	S247P	possibly damaging	Het
Trav23	A	T	14: 54,215,025 (GRCm39)	R79S	probably damaging	Het
Trf	C	A	9: 103,102,347 (GRCm39)	C177F	probably damaging	Het
Triml1	T	C	8: 43,589,408 (GRCm39)	Y260C	probably benign	Het
Tulp4	T	C	17: 6,286,510 (GRCm39)	F1513L	probably benign	Het
Umodl1	G	A	17: 31,205,090 (GRCm39)	V562I	probably damaging	Het
Ush2a	A	G	1: 188,491,960 (GRCm39)	K3083R	possibly damaging	Het
Vmn1r74	A	T	7: 11,580,888 (GRCm39)	I63F	probably benign	Het
Vmn2r38	C	T	7: 9,100,637 (GRCm39)	C43Y	possibly damaging	Het
Vmn2r50	A	T	7: 9,787,010 (GRCm39)	N32K	probably benign	Het
Vps13d	A	G	4: 144,784,032 (GRCm39)	V3914A		Het
Vwa5b2	A	G	16: 20,422,878 (GRCm39)	T984A	probably benign	Het
Zc3h3	C	T	15: 75,712,231 (GRCm39)	V77M	probably damaging	Het
Zfp397	A	T	18: 24,093,415 (GRCm39)	H300L	probably damaging	Het
Zfp950	G	A	19: 61,107,650 (GRCm39)	R478C	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
R6153:Nelfa	UTSW	5	34,056,223 (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'- GTATCTGCTCAGGTCACTCAG -3'
(R):5'- GACGGCAAACAAGGTCACTC -3'

Sequencing Primer
(F):5'- GCTCAGGTCACTCAGCACAAC -3'
(R):5'- ACGGTCTGTGCTAATGCTAAGC -3'

Posted On

2019-06-26