Incidental Mutation 'R4246:Nelfa'
| ID |
320417 |
| 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 |
041062-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4246 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
34055263-34093615 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 34056373 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Serine
at position 464
(F464S)
|
| 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: F464S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000030993
Gene: ENSMUSG00000029111
AA Change: F464S
| 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: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
| 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: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2700062C07Rik |
A |
G |
18: 24,606,013 (GRCm39) |
N36S |
possibly damaging |
Het |
| Ak1 |
A |
G |
2: 32,523,384 (GRCm39) |
T151A |
possibly damaging |
Het |
| Asxl3 |
A |
G |
18: 22,658,557 (GRCm39) |
D2189G |
probably damaging |
Het |
| Ccdc91 |
C |
T |
6: 147,493,646 (GRCm39) |
A346V |
unknown |
Het |
| Dnah6 |
C |
T |
6: 73,106,431 (GRCm39) |
E1769K |
probably benign |
Het |
| Dock6 |
A |
T |
9: 21,750,786 (GRCm39) |
|
probably null |
Het |
| Fhod3 |
A |
G |
18: 25,123,123 (GRCm39) |
K271R |
probably null |
Het |
| Glyatl3 |
T |
A |
17: 41,220,989 (GRCm39) |
D126V |
probably benign |
Het |
| Gnal |
C |
G |
18: 67,221,654 (GRCm39) |
P19R |
unknown |
Het |
| Igkv8-21 |
T |
A |
6: 70,292,436 (GRCm39) |
M1L |
possibly damaging |
Het |
| Itih4 |
C |
A |
14: 30,613,359 (GRCm39) |
H261N |
probably damaging |
Het |
| Jpt1 |
T |
C |
11: 115,405,119 (GRCm39) |
|
probably benign |
Het |
| Kif14 |
G |
T |
1: 136,401,126 (GRCm39) |
M492I |
possibly damaging |
Het |
| Klhl32 |
A |
C |
4: 24,800,822 (GRCm39) |
S3A |
possibly damaging |
Het |
| Kmt2d |
C |
T |
15: 98,737,970 (GRCm39) |
|
probably benign |
Het |
| Lamtor5 |
T |
C |
3: 107,186,354 (GRCm39) |
V41A |
probably benign |
Het |
| Lmtk3 |
G |
A |
7: 45,443,486 (GRCm39) |
C723Y |
possibly damaging |
Het |
| Lrfn1 |
G |
T |
7: 28,159,367 (GRCm39) |
V429L |
probably benign |
Het |
| Mapkbp1 |
T |
A |
2: 119,843,508 (GRCm39) |
I252N |
probably damaging |
Het |
| Nipbl |
G |
A |
15: 8,361,916 (GRCm39) |
L1454F |
probably damaging |
Het |
| Nr4a3 |
C |
T |
4: 48,083,125 (GRCm39) |
P553S |
possibly damaging |
Het |
| Nrg3 |
G |
A |
14: 39,194,198 (GRCm39) |
T187I |
possibly damaging |
Het |
| Or5m5 |
T |
A |
2: 85,814,624 (GRCm39) |
C147S |
possibly damaging |
Het |
| Or8g36 |
A |
G |
9: 39,422,899 (GRCm39) |
V39A |
probably benign |
Het |
| Pcdha8 |
A |
G |
18: 37,125,950 (GRCm39) |
E144G |
probably damaging |
Het |
| Pik3cb |
T |
C |
9: 98,983,229 (GRCm39) |
|
probably null |
Het |
| Pira1 |
C |
T |
7: 3,740,348 (GRCm39) |
G291E |
probably damaging |
Het |
| Pkd1l1 |
C |
T |
11: 8,815,543 (GRCm39) |
R1456K |
possibly damaging |
Het |
| Ppp1r3a |
T |
A |
6: 14,719,780 (GRCm39) |
E378V |
probably damaging |
Het |
| Psd2 |
T |
C |
18: 36,139,172 (GRCm39) |
L540P |
probably damaging |
Het |
| Rnf14 |
T |
A |
18: 38,434,701 (GRCm39) |
|
probably null |
Het |
| Satl1 |
A |
G |
X: 111,316,033 (GRCm39) |
S141P |
probably benign |
Het |
| Setx |
GTGGCT |
GT |
2: 29,044,073 (GRCm39) |
1814 |
probably null |
Het |
| Sh3d19 |
G |
A |
3: 86,033,995 (GRCm39) |
V783I |
probably benign |
Het |
| Snca |
T |
C |
6: 60,710,149 (GRCm39) |
E110G |
possibly damaging |
Het |
| Sumf1 |
A |
C |
6: 108,131,974 (GRCm39) |
V156G |
probably damaging |
Het |
| Trhr |
A |
T |
15: 44,096,856 (GRCm39) |
|
probably null |
Het |
| Tsen2 |
A |
G |
6: 115,524,785 (GRCm39) |
|
probably benign |
Het |
| Tuft1 |
C |
A |
3: 94,522,108 (GRCm39) |
M319I |
probably benign |
Het |
| Vill |
C |
A |
9: 118,889,461 (GRCm39) |
N132K |
probably damaging |
Het |
| Wars2 |
T |
A |
3: 99,123,904 (GRCm39) |
V255E |
probably damaging |
Het |
| Zcchc14 |
CTGATGGTGGTGGTGATGGTGGTGG |
CTGATGGTGGTGG |
8: 122,331,031 (GRCm39) |
|
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 |
|
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'- ACTGTGTCCACTAGCATGGTG -3'
(R):5'- GAGGAATGATTCTTTCAGGGGCAG -3'
Sequencing Primer
(F):5'- ACTAGCATGGTGGTACTGCC -3'
(R):5'- TTCTTTCAGGGGCAGACATAAGC -3'
|
| Posted On |
2015-06-12 |
Incidental Mutation