Incidental Mutation 'R2040:Nelfcd'
ID 225492
Institutional Source Beutler Lab
Gene Symbol Nelfcd
Ensembl Gene ENSMUSG00000016253
Gene Name negative elongation factor complex member C/D, Th1l
Synonyms Th1l, 2410003I03Rik, trihydrophobin 1
MMRRC Submission 040047-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.945) question?
Stock # R2040 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 174257623-174269298 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 174261875 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Tyrosine at position 48 (C48Y)
Ref Sequence ENSEMBL: ENSMUSP00000104703 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000016397] [ENSMUST00000109075]
AlphaFold Q922L6
Predicted Effect probably damaging
Transcript: ENSMUST00000016397
AA Change: C48Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000016397
Gene: ENSMUSG00000016253
AA Change: C48Y

DomainStartEndE-ValueType
Pfam:TH1 11 604 6.5e-276 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000109075
AA Change: C48Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000104703
Gene: ENSMUSG00000016253
AA Change: C48Y

DomainStartEndE-ValueType
Pfam:TH1 10 590 5.6e-303 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129716
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139390
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143683
Meta Mutation Damage Score 0.3408 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.1%
Validation Efficiency 99% (67/68)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The NELF complex of proteins interacts with the DSIF protein complex to repress transcriptional elongation by RNA polymerase II. The protein encoded by this gene is an essential part of the NELF complex. Alternative translation initiation site usage results in the formation of two isoforms with different N-termini. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700028K03Rik A T 5: 107,693,607 (GRCm39) I75L probably benign Het
Abca2 T C 2: 25,333,817 (GRCm39) L1755P probably damaging Het
Adam6b A T 12: 113,454,364 (GRCm39) I394L probably benign Het
Ano2 T A 6: 126,016,471 (GRCm39) N1001K probably benign Het
Arap2 A T 5: 62,906,259 (GRCm39) N253K probably damaging Het
Ascc3 T C 10: 50,604,227 (GRCm39) C1316R probably benign Het
Atox1 T C 11: 55,341,343 (GRCm39) Y64C probably benign Het
Atp13a1 A G 8: 70,259,702 (GRCm39) T1098A possibly damaging Het
Casr T C 16: 36,330,728 (GRCm39) E202G possibly damaging Het
Cct2 T C 10: 116,889,018 (GRCm39) T494A probably benign Het
Cd209e T A 8: 3,899,158 (GRCm39) N185Y probably damaging Het
Celsr1 A G 15: 85,917,088 (GRCm39) L295P probably damaging Het
Cyp26a1 A G 19: 37,686,499 (GRCm39) T48A possibly damaging Het
Elovl3 A G 19: 46,121,567 (GRCm39) S37G probably benign Het
Fbh1 T G 2: 11,774,706 (GRCm39) D13A possibly damaging Het
Fpr-rs4 CAGGAA CA 17: 18,242,596 (GRCm39) probably null Het
Frem3 G T 8: 81,342,455 (GRCm39) V1583L possibly damaging Het
Gm21863 C A 12: 20,004,515 (GRCm39) Q4K possibly damaging Het
Gm266 T C 12: 111,452,132 (GRCm39) T25A possibly damaging Het
Gm8674 T C 13: 50,055,705 (GRCm39) noncoding transcript Het
Greb1 T C 12: 16,752,651 (GRCm39) H897R probably damaging Het
Hells A G 19: 38,943,474 (GRCm39) D565G probably damaging Het
Hfm1 C T 5: 107,049,684 (GRCm39) V426I probably damaging Het
Ints6 G A 14: 62,951,138 (GRCm39) T297I probably damaging Het
Itga10 C T 3: 96,559,054 (GRCm39) probably benign Het
Kmt2b A T 7: 30,268,845 (GRCm39) M2628K probably damaging Het
Ktn1 T G 14: 47,938,069 (GRCm39) probably benign Het
Lyst T A 13: 13,815,807 (GRCm39) D1230E probably benign Het
Mboat1 T C 13: 30,425,300 (GRCm39) probably null Het
Moxd2 T C 6: 40,861,887 (GRCm39) probably null Het
Mtmr4 T C 11: 87,495,916 (GRCm39) M527T probably damaging Het
Myt1 T A 2: 181,467,717 (GRCm39) N1050K probably damaging Het
Ncoa6 A T 2: 155,248,000 (GRCm39) V1768E probably damaging Het
Opn3 G A 1: 175,491,145 (GRCm39) A296V possibly damaging Het
Or13a22 T C 7: 140,073,295 (GRCm39) I248T probably benign Het
Or2z8 T A 8: 72,811,607 (GRCm39) F28I possibly damaging Het
Pam T C 1: 97,792,167 (GRCm39) E418G possibly damaging Het
Prrc2c A T 1: 162,525,126 (GRCm39) N493K probably damaging Het
Ptpn18 A G 1: 34,509,300 (GRCm39) Q165R probably damaging Het
Ptpro C A 6: 137,363,162 (GRCm39) probably benign Het
Ralgapa1 A G 12: 55,833,107 (GRCm39) F132S probably damaging Het
Robo1 T C 16: 72,730,630 (GRCm39) C244R probably damaging Het
Robo3 A C 9: 37,338,760 (GRCm39) V316G probably damaging Het
Rsl1 T C 13: 67,330,145 (GRCm39) S198P probably damaging Het
Rsph9 T C 17: 46,445,910 (GRCm39) D220G probably damaging Het
Rxfp2 A C 5: 149,993,677 (GRCm39) I580L probably benign Het
Septin7 G A 9: 25,199,532 (GRCm39) A144T possibly damaging Het
Sfn T C 4: 133,328,603 (GRCm39) K160E probably benign Het
Ski A G 4: 155,306,029 (GRCm39) Y317H probably damaging Het
Skic3 A C 13: 76,328,222 (GRCm39) R1423S probably damaging Het
Slc22a22 A T 15: 57,110,936 (GRCm39) Y430* probably null Het
Src A G 2: 157,299,030 (GRCm39) K9R probably benign Het
Srm C T 4: 148,678,453 (GRCm39) P255L possibly damaging Het
Stpg4 T A 17: 87,730,075 (GRCm39) N90I probably damaging Het
Sytl2 T A 7: 90,031,069 (GRCm39) probably benign Het
Tbpl2 T C 2: 23,984,871 (GRCm39) K92R probably benign Het
Tlcd4 G T 3: 121,024,975 (GRCm39) probably benign Het
Tmem38a T A 8: 73,335,096 (GRCm39) N178K probably damaging Het
Tnfaip3 T C 10: 18,883,900 (GRCm39) D160G possibly damaging Het
Vegfb T A 19: 6,963,407 (GRCm39) H119L possibly damaging Het
Vmn2r111 T A 17: 22,767,395 (GRCm39) I701F probably damaging Het
Vmn2r95 C T 17: 18,661,561 (GRCm39) L436F probably damaging Het
Wdr47 T C 3: 108,530,688 (GRCm39) C394R probably benign Het
Ythdc2 T A 18: 44,988,241 (GRCm39) Y16* probably null Het
Zer1 G A 2: 29,998,286 (GRCm39) L342F probably damaging Het
Zfp353-ps A G 8: 42,535,333 (GRCm39) noncoding transcript Het
Other mutations in Nelfcd
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01999:Nelfcd APN 2 174,265,308 (GRCm39) splice site probably benign
IGL02175:Nelfcd APN 2 174,262,175 (GRCm39) missense probably benign 0.01
IGL02955:Nelfcd APN 2 174,264,391 (GRCm39) missense probably damaging 0.98
IGL03193:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03194:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03203:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03217:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03237:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03273:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03278:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03289:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03365:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03398:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03405:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
IGL03407:Nelfcd APN 2 174,268,625 (GRCm39) missense possibly damaging 0.87
R0593:Nelfcd UTSW 2 174,265,223 (GRCm39) missense probably benign 0.00
R0751:Nelfcd UTSW 2 174,264,807 (GRCm39) missense probably benign 0.03
R1852:Nelfcd UTSW 2 174,265,771 (GRCm39) splice site probably null
R3606:Nelfcd UTSW 2 174,268,337 (GRCm39) missense probably benign 0.10
R3716:Nelfcd UTSW 2 174,264,798 (GRCm39) missense possibly damaging 0.51
R4235:Nelfcd UTSW 2 174,268,841 (GRCm39) missense probably damaging 1.00
R4607:Nelfcd UTSW 2 174,264,955 (GRCm39) missense probably benign 0.01
R4775:Nelfcd UTSW 2 174,268,369 (GRCm39) missense probably damaging 0.96
R5104:Nelfcd UTSW 2 174,268,159 (GRCm39) missense probably benign 0.10
R5859:Nelfcd UTSW 2 174,268,856 (GRCm39) makesense probably null
R6025:Nelfcd UTSW 2 174,268,611 (GRCm39) missense probably damaging 1.00
R6104:Nelfcd UTSW 2 174,265,250 (GRCm39) missense probably damaging 0.99
R6280:Nelfcd UTSW 2 174,257,739 (GRCm39) missense probably benign
R7249:Nelfcd UTSW 2 174,264,999 (GRCm39) critical splice donor site probably null
R7382:Nelfcd UTSW 2 174,265,176 (GRCm39) missense probably benign 0.00
R7532:Nelfcd UTSW 2 174,268,189 (GRCm39) missense probably damaging 1.00
R7545:Nelfcd UTSW 2 174,265,771 (GRCm39) splice site probably null
R7766:Nelfcd UTSW 2 174,268,625 (GRCm39) missense possibly damaging 0.87
R9011:Nelfcd UTSW 2 174,268,717 (GRCm39) missense probably benign 0.15
R9094:Nelfcd UTSW 2 174,265,861 (GRCm39) missense probably damaging 1.00
R9332:Nelfcd UTSW 2 174,264,978 (GRCm39) missense probably benign 0.02
R9486:Nelfcd UTSW 2 174,268,635 (GRCm39) missense probably damaging 1.00
R9695:Nelfcd UTSW 2 174,266,923 (GRCm39) missense probably benign 0.34
Z1088:Nelfcd UTSW 2 174,268,287 (GRCm39) frame shift probably null
Predicted Primers PCR Primer
(F):5'- GGTTCCTGACCCCTTTGAAG -3'
(R):5'- CAGCTTTTACACTGAGGGGAC -3'

Sequencing Primer
(F):5'- GAAGCTGCCTCTTGTCTAGC -3'
(R):5'- CTGGGGTAGACAGGTGGGC -3'
Posted On 2014-08-25