Incidental Mutation 'R4398:Nelfa'
ID |
374382 |
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 |
041130-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R4398 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
34055263-34093615 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 34058623 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Glycine
at position 279
(D279G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000030993
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030993]
[ENSMUST00000066854]
[ENSMUST00000075812]
[ENSMUST00000137191]
[ENSMUST00000139845]
|
AlphaFold |
Q8BG30 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000030993
AA Change: D279G
PolyPhen 2
Score 0.656 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000030993 Gene: ENSMUSG00000029111 AA Change: D279G
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: 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 |
noncoding transcript
Transcript: ENSMUST00000183676
|
Meta Mutation Damage Score |
0.1474 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.7%
|
Validation Efficiency |
96% (53/55) |
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: 47 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adamts20 |
C |
A |
15: 94,231,576 (GRCm39) |
R871L |
possibly damaging |
Het |
Adcy5 |
G |
A |
16: 35,089,363 (GRCm39) |
C520Y |
probably damaging |
Het |
AI661453 |
G |
A |
17: 47,779,042 (GRCm39) |
|
probably benign |
Het |
Bptf |
T |
C |
11: 107,001,670 (GRCm39) |
K481E |
probably damaging |
Het |
Cnot10 |
T |
A |
9: 114,460,949 (GRCm39) |
K74* |
probably null |
Het |
Ctc1 |
C |
T |
11: 68,913,697 (GRCm39) |
P200S |
probably damaging |
Het |
Dact1 |
T |
C |
12: 71,363,959 (GRCm39) |
Y210H |
probably damaging |
Het |
Dbn1 |
T |
C |
13: 55,623,194 (GRCm39) |
T430A |
probably benign |
Het |
Dmd |
A |
C |
X: 82,765,624 (GRCm39) |
T657P |
probably benign |
Het |
Efnb2 |
C |
T |
8: 8,670,832 (GRCm39) |
R256H |
possibly damaging |
Het |
Eif4a1 |
T |
C |
11: 69,560,070 (GRCm39) |
I116M |
possibly damaging |
Het |
F730035P03Rik |
A |
T |
7: 99,429,475 (GRCm39) |
|
noncoding transcript |
Het |
Fbn1 |
C |
T |
2: 125,239,701 (GRCm39) |
V329I |
probably benign |
Het |
Gpr20 |
G |
A |
15: 73,568,125 (GRCm39) |
T88I |
probably benign |
Het |
Herc1 |
T |
G |
9: 66,386,735 (GRCm39) |
V3783G |
probably benign |
Het |
Khdc1a |
A |
G |
1: 21,420,617 (GRCm39) |
D79G |
possibly damaging |
Het |
Klk1b16 |
A |
T |
7: 43,790,851 (GRCm39) |
I218F |
probably damaging |
Het |
Malrd1 |
C |
T |
2: 16,155,594 (GRCm39) |
T2001I |
unknown |
Het |
Mia3 |
A |
G |
1: 183,111,733 (GRCm39) |
S556P |
probably damaging |
Het |
Myo3a |
T |
A |
2: 22,467,854 (GRCm39) |
D369E |
probably benign |
Het |
Ntrk3 |
A |
T |
7: 77,900,517 (GRCm39) |
C607* |
probably null |
Het |
Or13a20 |
T |
C |
7: 140,232,741 (GRCm39) |
V283A |
possibly damaging |
Het |
Pclo |
A |
T |
5: 14,825,380 (GRCm39) |
Q1371L |
probably damaging |
Het |
Pdzd2 |
A |
T |
15: 12,376,061 (GRCm39) |
V1358E |
probably benign |
Het |
Pgr |
T |
C |
9: 8,903,750 (GRCm39) |
|
probably null |
Het |
Prag1 |
A |
G |
8: 36,570,809 (GRCm39) |
D464G |
probably damaging |
Het |
Prickle4 |
A |
G |
17: 48,001,456 (GRCm39) |
|
probably benign |
Het |
Prim2 |
A |
G |
1: 33,551,192 (GRCm39) |
Y309H |
probably damaging |
Het |
Prkaa1 |
A |
G |
15: 5,206,642 (GRCm39) |
Q464R |
possibly damaging |
Het |
Rab36 |
G |
A |
10: 74,880,328 (GRCm39) |
V63I |
probably damaging |
Het |
Rint1 |
T |
A |
5: 23,999,445 (GRCm39) |
I78K |
possibly damaging |
Het |
Rnf130 |
T |
A |
11: 49,962,205 (GRCm39) |
F217Y |
probably benign |
Het |
Smad7 |
T |
C |
18: 75,527,234 (GRCm39) |
V360A |
probably damaging |
Het |
Sp110 |
A |
C |
1: 85,505,050 (GRCm39) |
F434C |
probably benign |
Het |
Stag1 |
A |
G |
9: 100,838,659 (GRCm39) |
|
probably benign |
Het |
Tlr12 |
T |
A |
4: 128,509,988 (GRCm39) |
D754V |
probably benign |
Het |
Tmf1 |
G |
A |
6: 97,155,857 (GRCm39) |
P43L |
probably damaging |
Het |
Togaram1 |
A |
G |
12: 65,027,630 (GRCm39) |
N873S |
probably benign |
Het |
Tsn |
C |
T |
1: 118,238,799 (GRCm39) |
|
probably benign |
Het |
Ubn1 |
A |
G |
16: 4,882,289 (GRCm39) |
K250R |
probably damaging |
Het |
Vmn1r25 |
A |
T |
6: 57,955,812 (GRCm39) |
V159D |
probably damaging |
Het |
Vmn2r89 |
T |
C |
14: 51,689,551 (GRCm39) |
L18P |
probably damaging |
Het |
Vps8 |
T |
G |
16: 21,323,216 (GRCm39) |
N689K |
probably damaging |
Het |
Ythdc1 |
T |
A |
5: 86,963,513 (GRCm39) |
D30E |
possibly damaging |
Het |
Ythdc1 |
G |
T |
5: 86,983,679 (GRCm39) |
|
probably benign |
Het |
Zfp407 |
G |
A |
18: 84,580,856 (GRCm39) |
Q86* |
probably null |
Het |
Zfp521 |
C |
T |
18: 13,979,601 (GRCm39) |
E271K |
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 |
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'- GGCAGTAATCCTAGAATGAGGC -3'
(R):5'- GCTTCTGCCAGTATAGAGTGGG -3'
Sequencing Primer
(F):5'- GGCAGGTATTTGTTCCAAACACG -3'
(R):5'- ACAAGGTCTGTACACTGTGGTCC -3'
|
Posted On |
2016-03-02 |