Incidental Mutation 'R0635:Hdgfl2'
ID 56642
Institutional Source Beutler Lab
Gene Symbol Hdgfl2
Ensembl Gene ENSMUSG00000002833
Gene Name HDGF like 2
Synonyms HRP-2, Hdgfrp2
MMRRC Submission 038824-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.146) question?
Stock # R0635 (G1)
Quality Score 194
Status Validated
Chromosome 17
Chromosomal Location 56386634-56407607 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 56403057 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 177 (L177Q)
Ref Sequence ENSEMBL: ENSMUSP00000152948 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002908] [ENSMUST00000002911] [ENSMUST00000190703] [ENSMUST00000226053] [ENSMUST00000225843]
AlphaFold Q3UMU9
Predicted Effect probably benign
Transcript: ENSMUST00000002908
SMART Domains Protein: ENSMUSP00000002908
Gene: ENSMUSG00000002831

DomainStartEndE-ValueType
low complexity region 19 31 N/A INTRINSIC
internal_repeat_2 74 335 9.44e-7 PROSPERO
internal_repeat_1 103 467 2.72e-12 PROSPERO
internal_repeat_2 343 701 9.44e-7 PROSPERO
internal_repeat_1 598 1090 2.72e-12 PROSPERO
low complexity region 1124 1136 N/A INTRINSIC
Pfam:Perilipin 1144 1385 2.3e-22 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000002911
AA Change: L177Q

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000002911
Gene: ENSMUSG00000002833
AA Change: L177Q

DomainStartEndE-ValueType
PWWP 5 62 1.78e-19 SMART
low complexity region 90 109 N/A INTRINSIC
low complexity region 127 136 N/A INTRINSIC
low complexity region 137 153 N/A INTRINSIC
low complexity region 163 175 N/A INTRINSIC
low complexity region 181 196 N/A INTRINSIC
low complexity region 212 243 N/A INTRINSIC
low complexity region 252 272 N/A INTRINSIC
low complexity region 273 300 N/A INTRINSIC
low complexity region 301 311 N/A INTRINSIC
coiled coil region 321 364 N/A INTRINSIC
low complexity region 398 411 N/A INTRINSIC
Pfam:LEDGF 468 569 2.8e-31 PFAM
internal_repeat_1 575 644 2.5e-5 PROSPERO
Predicted Effect probably benign
Transcript: ENSMUST00000190703
SMART Domains Protein: ENSMUSP00000139859
Gene: ENSMUSG00000002831

DomainStartEndE-ValueType
low complexity region 19 31 N/A INTRINSIC
internal_repeat_2 74 335 9.44e-7 PROSPERO
internal_repeat_1 103 467 2.72e-12 PROSPERO
internal_repeat_2 343 701 9.44e-7 PROSPERO
internal_repeat_1 598 1090 2.72e-12 PROSPERO
Pfam:Perilipin 1110 1385 1.4e-16 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224101
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224172
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224655
Predicted Effect probably damaging
Transcript: ENSMUST00000226053
AA Change: L177Q

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
Predicted Effect probably damaging
Transcript: ENSMUST00000225843
AA Change: L177Q

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000225208
Predicted Effect noncoding transcript
Transcript: ENSMUST00000226035
Predicted Effect noncoding transcript
Transcript: ENSMUST00000225342
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224701
Predicted Effect noncoding transcript
Transcript: ENSMUST00000225731
Meta Mutation Damage Score 0.0678 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.8%
  • 10x: 97.4%
  • 20x: 94.9%
Validation Efficiency 99% (68/69)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the hepatoma-derived growth factor (HDGF) family. The protein includes an N-terminal PWWP domain that binds to methyl-lysine-containing histones, with specific binding of this protein to tri-methylated lysines 36 and 79 of histone H3, and di- and tri-methylated lysine 20 of histone H4. The protein functions in LEDGF/p75-independent HIV-1 replication by determining HIV-1 integration site selection. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2014]
PHENOTYPE: Homozygous mice exhibit an increased mean serum alkaline phosphatase level compared to controls. Female mutants exhibited a decreased mean skin fibroblast proliferation rate. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5730455P16Rik A T 11: 80,264,891 (GRCm39) probably benign Het
Adamts15 A G 9: 30,816,066 (GRCm39) L631P probably damaging Het
Adamts17 T C 7: 66,558,353 (GRCm39) F266L probably damaging Het
Adgrb1 C A 15: 74,412,741 (GRCm39) Q488K possibly damaging Het
Armh4 A G 14: 50,010,600 (GRCm39) L369S probably benign Het
Cep290 A G 10: 100,328,538 (GRCm39) D109G probably damaging Het
Chil5 A T 3: 105,924,519 (GRCm39) Y229N possibly damaging Het
Cntnap1 A G 11: 101,074,285 (GRCm39) T742A probably benign Het
Col6a3 A T 1: 90,735,808 (GRCm39) probably null Het
Col6a5 G A 9: 105,805,805 (GRCm39) P1034S unknown Het
Daxx T A 17: 34,131,618 (GRCm39) D442E probably benign Het
Dmxl1 T C 18: 49,984,490 (GRCm39) probably benign Het
Dnah11 A G 12: 117,971,731 (GRCm39) F2942S probably damaging Het
Garin4 T C 1: 190,895,924 (GRCm39) T240A probably benign Het
Glg1 A G 8: 111,890,396 (GRCm39) probably benign Het
Gm10272 G A 10: 77,542,535 (GRCm39) probably benign Het
Gm17333 AAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAA AAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAA 16: 77,649,766 (GRCm39) noncoding transcript Het
Haao A G 17: 84,146,003 (GRCm39) F83S probably damaging Het
Hrh1 T C 6: 114,457,106 (GRCm39) V129A probably damaging Het
Ift43 T A 12: 86,131,855 (GRCm39) probably benign Het
Il21r T C 7: 125,231,678 (GRCm39) Y369H probably damaging Het
Il2ra C T 2: 11,685,177 (GRCm39) T171M probably benign Het
Lao1 C T 4: 118,825,493 (GRCm39) R438C probably benign Het
Lrrcc1 G A 3: 14,624,288 (GRCm39) S350N probably benign Het
Mageb5 T A X: 90,823,599 (GRCm39) Y260F probably benign Het
Marchf5 A T 19: 37,197,807 (GRCm39) I159F possibly damaging Het
Mgat4a G A 1: 37,491,375 (GRCm39) A282V probably benign Het
Mipep G A 14: 61,066,839 (GRCm39) V420I probably damaging Het
Morc2b A T 17: 33,356,661 (GRCm39) F370L possibly damaging Het
Mt1 A T 8: 94,906,449 (GRCm39) probably null Het
Ncapd2 A G 6: 125,149,999 (GRCm39) V943A probably benign Het
Nkd2 T C 13: 73,975,013 (GRCm39) D58G probably benign Het
Nol8 C G 13: 49,830,234 (GRCm39) S1106C probably benign Het
Nrm C A 17: 36,175,156 (GRCm39) Y61* probably null Het
Nusap1 A G 2: 119,458,148 (GRCm39) T95A probably damaging Het
Ocln T A 13: 100,642,744 (GRCm39) Q197L probably damaging Het
Or5p70 T A 7: 107,994,971 (GRCm39) F215I probably benign Het
Oxtr A G 6: 112,466,161 (GRCm39) Y200H probably damaging Het
Paip2b T C 6: 83,786,891 (GRCm39) E115G possibly damaging Het
Pcm1 T A 8: 41,720,216 (GRCm39) probably benign Het
Pcnt T C 10: 76,240,419 (GRCm39) D1205G probably damaging Het
Phka1 G A X: 101,665,006 (GRCm39) R186C probably damaging Het
Pik3cb A G 9: 98,946,271 (GRCm39) probably benign Het
Pik3r1 C T 13: 101,893,926 (GRCm39) R81K probably benign Het
Ppa1 A G 10: 61,501,219 (GRCm39) D162G probably benign Het
Ppa1 A G 10: 61,502,749 (GRCm39) R191G probably damaging Het
Ppp4r3c2 T C X: 88,796,128 (GRCm39) probably benign Het
Prss22 T A 17: 24,215,662 (GRCm39) T87S probably benign Het
Rgr T A 14: 36,760,904 (GRCm39) R218* probably null Het
Rreb1 A T 13: 38,125,540 (GRCm39) Q1282L possibly damaging Het
Scel T A 14: 103,820,575 (GRCm39) probably null Het
Sema6b A G 17: 56,436,971 (GRCm39) probably null Het
Slc4a1 T C 11: 102,243,498 (GRCm39) E711G possibly damaging Het
Snx19 C A 9: 30,340,106 (GRCm39) L415M probably damaging Het
Snx19 T G 9: 30,340,107 (GRCm39) L415R probably damaging Het
Specc1 G A 11: 62,009,729 (GRCm39) R495Q probably damaging Het
Tead1 T C 7: 112,490,913 (GRCm39) probably benign Het
Timm10b A C 7: 105,289,895 (GRCm39) probably benign Het
Ubxn7 T A 16: 32,186,235 (GRCm39) probably benign Het
Vmn2r116 T A 17: 23,605,861 (GRCm39) Y258N possibly damaging Het
Vmn2r77 T A 7: 86,460,383 (GRCm39) F570I probably benign Het
Vmn2r98 T C 17: 19,300,759 (GRCm39) V587A probably benign Het
Zfp398 T C 6: 47,840,074 (GRCm39) I101T probably damaging Het
Zfp808 T A 13: 62,320,233 (GRCm39) H487Q probably damaging Het
Other mutations in Hdgfl2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01446:Hdgfl2 APN 17 56,404,281 (GRCm39) missense possibly damaging 0.94
IGL01486:Hdgfl2 APN 17 56,405,733 (GRCm39) missense possibly damaging 0.84
IGL02977:Hdgfl2 APN 17 56,406,319 (GRCm39) missense possibly damaging 0.71
IGL03196:Hdgfl2 APN 17 56,400,607 (GRCm39) missense probably benign 0.40
IGL03368:Hdgfl2 APN 17 56,386,746 (GRCm39) utr 5 prime probably benign
R0325:Hdgfl2 UTSW 17 56,406,181 (GRCm39) missense possibly damaging 0.95
R1914:Hdgfl2 UTSW 17 56,403,978 (GRCm39) missense probably damaging 1.00
R1927:Hdgfl2 UTSW 17 56,406,874 (GRCm39) missense possibly damaging 0.92
R2157:Hdgfl2 UTSW 17 56,405,691 (GRCm39) missense possibly damaging 0.46
R2337:Hdgfl2 UTSW 17 56,403,987 (GRCm39) missense possibly damaging 0.46
R4884:Hdgfl2 UTSW 17 56,403,265 (GRCm39) missense possibly damaging 0.91
R5093:Hdgfl2 UTSW 17 56,406,217 (GRCm39) missense possibly damaging 0.92
R5510:Hdgfl2 UTSW 17 56,389,118 (GRCm39) missense possibly damaging 0.77
R6862:Hdgfl2 UTSW 17 56,406,211 (GRCm39) missense probably damaging 0.97
R7180:Hdgfl2 UTSW 17 56,404,532 (GRCm39) splice site probably null
R7389:Hdgfl2 UTSW 17 56,406,389 (GRCm39) critical splice donor site probably null
R7564:Hdgfl2 UTSW 17 56,406,860 (GRCm39) missense unknown
R7921:Hdgfl2 UTSW 17 56,400,724 (GRCm39) critical splice donor site probably null
R8168:Hdgfl2 UTSW 17 56,389,282 (GRCm39) missense probably damaging 0.98
R8348:Hdgfl2 UTSW 17 56,406,370 (GRCm39) missense possibly damaging 0.82
R8415:Hdgfl2 UTSW 17 56,400,712 (GRCm39) missense probably benign 0.19
R9070:Hdgfl2 UTSW 17 56,389,371 (GRCm39) missense possibly damaging 0.76
R9541:Hdgfl2 UTSW 17 56,405,976 (GRCm39) missense unknown
R9657:Hdgfl2 UTSW 17 56,405,978 (GRCm39) missense unknown
Z1176:Hdgfl2 UTSW 17 56,404,016 (GRCm39) missense probably null
Z1176:Hdgfl2 UTSW 17 56,386,825 (GRCm39) missense possibly damaging 0.79
Z1177:Hdgfl2 UTSW 17 56,406,343 (GRCm39) missense unknown
Predicted Primers PCR Primer
(F):5'- GTGAAAGTTCCAGCCCCATCAGAC -3'
(R):5'- AAAAGGCCCCTCATGCTGCTTAG -3'

Sequencing Primer
(F):5'- TCTTCAGAGTGGGACCTACAG -3'
(R):5'- TGGGGCACAGAACCCTTAC -3'
Posted On 2013-07-11