Incidental Mutation 'R8446:Nelfa'
ID 654490
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 067827-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8446 (G1)
Quality Score 225.009
Status Not validated
Chromosome 5
Chromosomal Location 34055263-34093615 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 34058982 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 262 (L262Q)
Ref Sequence ENSEMBL: ENSMUSP00000030993 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030993] [ENSMUST00000066854] [ENSMUST00000075812] [ENSMUST00000137191] [ENSMUST00000139845]
AlphaFold Q8BG30
Predicted Effect probably damaging
Transcript: ENSMUST00000030993
AA Change: L262Q

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000030993
Gene: ENSMUSG00000029111
AA Change: L262Q

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.2%
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcf2 G A 5: 24,771,641 (GRCm39) R529* probably null Het
Afap1 T A 5: 36,144,645 (GRCm39) S122T Het
Arnt TG T 3: 95,382,014 (GRCm39) probably null Het
Bbs1 G A 19: 4,947,633 (GRCm39) T307I probably benign Het
Cacna1c A T 6: 118,604,411 (GRCm39) S1439T Het
Camk4 T A 18: 33,289,810 (GRCm39) H152Q probably damaging Het
Capn2 A T 1: 182,311,796 (GRCm39) M426K possibly damaging Het
Chrm3 C T 13: 9,928,338 (GRCm39) G233S probably damaging Het
Clca3a1 A T 3: 144,454,248 (GRCm39) Y461N probably damaging Het
Clip1 G C 5: 123,794,008 (GRCm39) P12A probably damaging Het
Cmya5 A G 13: 93,230,336 (GRCm39) L1584P possibly damaging Het
Commd5 T C 15: 76,785,094 (GRCm39) S164P probably damaging Het
Csgalnact1 A G 8: 68,913,743 (GRCm39) V154A probably damaging Het
Ddias C A 7: 92,515,818 (GRCm39) C25F probably damaging Het
Dnah7b A T 1: 46,329,875 (GRCm39) I3240F probably damaging Het
Fam186a T G 15: 99,845,335 (GRCm39) D303A unknown Het
Igkv8-27 A G 6: 70,148,932 (GRCm39) I74T probably damaging Het
Itgb2l G T 16: 96,233,857 (GRCm39) Q278K probably damaging Het
Itgb7 T C 15: 102,127,043 (GRCm39) E464G probably damaging Het
Kdm2a G A 19: 4,406,916 (GRCm39) Q116* probably null Het
Krtap5-2 TCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACCACAGCCCCCACAGGAACTACA TCCACAGGAACTACA 7: 141,728,845 (GRCm39) probably benign Het
Larp1 T C 11: 57,942,035 (GRCm39) probably null Het
Lnx2 A G 5: 146,970,169 (GRCm39) L191S probably benign Het
Mtmr7 G A 8: 41,059,927 (GRCm39) A62V possibly damaging Het
Myh4 T A 11: 67,144,347 (GRCm39) M1239K probably benign Het
Nckap5l C A 15: 99,323,930 (GRCm39) G858C probably benign Het
Or2j3 A G 17: 38,615,638 (GRCm39) V238A probably benign Het
Or8b46 A T 9: 38,450,964 (GRCm39) M258L probably benign Het
Pdgfa T C 5: 138,964,395 (GRCm39) T211A unknown Het
Prl3d2 A T 13: 27,307,976 (GRCm39) I86F probably benign Het
Rpf2 T A 10: 40,115,752 (GRCm39) T76S probably benign Het
Setbp1 C T 18: 78,900,971 (GRCm39) D899N probably damaging Het
Slc35c1 T A 2: 92,284,707 (GRCm39) E315D probably benign Het
Slc6a3 A T 13: 73,719,674 (GRCm39) M568L possibly damaging Het
Sorbs1 T C 19: 40,314,602 (GRCm39) M737V probably benign Het
Sox17 A G 1: 4,562,316 (GRCm39) Y295H possibly damaging Het
Tex44 A T 1: 86,354,696 (GRCm39) I202F possibly damaging Het
Tinagl1 C T 4: 130,060,694 (GRCm39) probably null Het
Tlr4 T A 4: 66,757,673 (GRCm39) N155K probably damaging Het
Tmem245 T C 4: 56,906,261 (GRCm39) Q548R probably benign Het
Topbp1 T A 9: 103,186,061 (GRCm39) F68I probably damaging Het
Trim67 G T 8: 125,520,730 (GRCm39) A31S probably damaging Het
Triobp C T 15: 78,878,326 (GRCm39) H1750Y possibly damaging Het
Ttn A C 2: 76,778,553 (GRCm39) M1316R unknown Het
Usp40 T C 1: 87,906,190 (GRCm39) T682A probably benign Het
Wfs1 A T 5: 37,128,953 (GRCm39) D272E probably benign Het
Zfp763 A T 17: 33,238,473 (GRCm39) M224K probably benign Het
Other mutations in Nelfa
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- TCTGTGAAGGCCAAATGCAAAATAG -3'
(R):5'- AGCGTCTTCAGTCCTTCTGG -3'

Sequencing Primer
(F):5'- CTATGCACTTAGGTCTCAGGGCAAG -3'
(R):5'- GGGAACCGGACTCCAATAC -3'
Posted On 2020-10-20