Incidental Mutation 'R7166:Hlcs'
ID 557959
Institutional Source Beutler Lab
Gene Symbol Hlcs
Ensembl Gene ENSMUSG00000040820
Gene Name holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)
Synonyms D16Jhu34, 410I21.SP6
MMRRC Submission 045227-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7166 (G1)
Quality Score 225.009
Status Validated
Chromosome 16
Chromosomal Location 93929741-94114430 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 94063585 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Asparagine at position 345 (D345N)
Ref Sequence ENSEMBL: ENSMUSP00000130981 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000099512] [ENSMUST00000163193] [ENSMUST00000227141]
AlphaFold Q920N2
Predicted Effect possibly damaging
Transcript: ENSMUST00000099512
AA Change: D345N

PolyPhen 2 Score 0.919 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000097112
Gene: ENSMUSG00000040820
AA Change: D345N

DomainStartEndE-ValueType
low complexity region 38 55 N/A INTRINSIC
low complexity region 377 391 N/A INTRINSIC
Pfam:BPL_LplA_LipB 467 599 1.9e-21 PFAM
Pfam:BPL_C 665 714 3.7e-12 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000163193
AA Change: D345N

PolyPhen 2 Score 0.919 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000130981
Gene: ENSMUSG00000040820
AA Change: D345N

DomainStartEndE-ValueType
low complexity region 38 55 N/A INTRINSIC
low complexity region 377 391 N/A INTRINSIC
Pfam:BPL_LplA_LipB 467 599 3.6e-30 PFAM
Pfam:BPL_C 665 714 4.9e-13 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000227141
AA Change: D492N

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 98% (52/53)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an enzyme that catalyzes the binding of biotin to carboxylases and histones. The protein plays an important role in gluconeogenesis, fatty acid synthesis and branched chain amino acid catabolism. Defects in this gene are the cause of holocarboxylase synthetase deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Jun 2011]
Allele List at MGI
Other mutations in this stock
Total: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ambn T C 5: 88,615,387 (GRCm39) L272P possibly damaging Het
Ash2l C A 8: 26,317,348 (GRCm39) G335V probably damaging Het
Atp13a1 T A 8: 70,251,966 (GRCm39) probably null Het
Atp13a2 G A 4: 140,734,295 (GRCm39) R1139Q possibly damaging Het
Atxn2 T A 5: 121,934,460 (GRCm39) N886K possibly damaging Het
Celsr3 G T 9: 108,720,150 (GRCm39) C2512F probably damaging Het
Cfap221 A G 1: 119,875,843 (GRCm39) V449A probably benign Het
Cfhr2 A T 1: 139,758,839 (GRCm39) C70* probably null Het
Chfr C A 5: 110,306,671 (GRCm39) P472Q probably benign Het
Crybg2 G A 4: 133,788,193 (GRCm39) R22Q probably damaging Het
Eef2k T C 7: 120,483,995 (GRCm39) F244L probably damaging Het
Efcab11 A T 12: 99,849,614 (GRCm39) M23K Het
Eif4a3l2 A G 6: 116,528,329 (GRCm39) I69V probably benign Het
Ercc8 T A 13: 108,305,967 (GRCm39) M114K possibly damaging Het
Fam217a T C 13: 35,094,298 (GRCm39) Y487C probably benign Het
Farsb T C 1: 78,447,821 (GRCm39) N205S probably benign Het
Glra1 A G 11: 55,405,904 (GRCm39) F370S probably benign Het
Gm12258 T A 11: 58,749,299 (GRCm39) M158K Het
Gm14305 T A 2: 176,412,736 (GRCm39) H209Q probably damaging Het
Gm4924 A T 10: 82,214,035 (GRCm39) Q611L unknown Het
H4c11 A G 13: 21,919,321 (GRCm39) H19R unknown Het
Haus6 T C 4: 86,501,924 (GRCm39) E649G possibly damaging Het
Htt C A 5: 35,010,238 (GRCm39) Q1564K probably benign Het
Itpr1 G A 6: 108,355,151 (GRCm39) V481I probably benign Het
Jak3 T C 8: 72,134,960 (GRCm39) I531T probably damaging Het
Kng1 T A 16: 22,898,428 (GRCm39) H609Q probably benign Het
Mdn1 T A 4: 32,746,446 (GRCm39) S4131T probably damaging Het
Npnt A G 3: 132,653,889 (GRCm39) S31P probably damaging Het
Or1r1 A T 11: 73,875,121 (GRCm39) F104L possibly damaging Het
Or4c100 A T 2: 88,355,990 (GRCm39) Q21L possibly damaging Het
Or8h8 T A 2: 86,753,092 (GRCm39) K261N probably damaging Het
Paxx A T 2: 25,350,238 (GRCm39) L123Q probably damaging Het
Prdm13 C T 4: 21,683,528 (GRCm39) R144Q unknown Het
Rab2b C A 14: 52,516,802 (GRCm39) probably benign Het
Rnf207 A G 4: 152,396,237 (GRCm39) I509T probably damaging Het
Ropn1l T C 15: 31,453,655 (GRCm39) Q12R Het
Ryr3 T G 2: 112,705,373 (GRCm39) Y847S probably damaging Het
Slc1a6 A T 10: 78,648,646 (GRCm39) T456S possibly damaging Het
Slc26a2 A T 18: 61,331,901 (GRCm39) M510K possibly damaging Het
Slc5a9 T C 4: 111,741,036 (GRCm39) T537A probably benign Het
Slc9b2 T C 3: 135,031,939 (GRCm39) Y132H unknown Het
Sltm T C 9: 70,492,132 (GRCm39) L725S probably damaging Het
Spz1 A G 13: 92,712,435 (GRCm39) C14R probably benign Het
Srrm4 T A 5: 116,609,301 (GRCm39) Q172L unknown Het
Synj2bp T C 12: 81,551,289 (GRCm39) D92G probably benign Het
Tmem169 A C 1: 72,340,229 (GRCm39) T220P probably benign Het
Ttn T A 2: 76,718,372 (GRCm39) I7270F unknown Het
Txndc16 T G 14: 45,420,611 (GRCm39) N137H probably benign Het
Ubr5 A G 15: 37,976,389 (GRCm39) Y2499H Het
Ugt2b38 T C 5: 87,558,305 (GRCm39) D452G probably damaging Het
Zfp12 T A 5: 143,231,257 (GRCm39) I560N possibly damaging Het
Zfp60 A G 7: 27,448,937 (GRCm39) K535R possibly damaging Het
Zfp960 T A 17: 17,308,761 (GRCm39) C492S probably damaging Het
Other mutations in Hlcs
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01078:Hlcs APN 16 93,934,019 (GRCm39) missense probably damaging 0.99
IGL02026:Hlcs APN 16 93,935,564 (GRCm39) missense probably damaging 0.99
IGL02341:Hlcs APN 16 94,031,969 (GRCm39) missense probably damaging 0.99
IGL03075:Hlcs APN 16 93,939,706 (GRCm39) missense probably damaging 1.00
PIT4515001:Hlcs UTSW 16 94,068,275 (GRCm39) missense probably benign 0.45
R0372:Hlcs UTSW 16 93,939,766 (GRCm39) missense possibly damaging 0.69
R0664:Hlcs UTSW 16 94,032,170 (GRCm39) missense probably damaging 1.00
R0731:Hlcs UTSW 16 93,932,711 (GRCm39) missense probably damaging 1.00
R1465:Hlcs UTSW 16 94,069,151 (GRCm39) missense probably damaging 0.99
R1465:Hlcs UTSW 16 94,069,151 (GRCm39) missense probably damaging 0.99
R1761:Hlcs UTSW 16 94,068,866 (GRCm39) missense probably benign 0.05
R2013:Hlcs UTSW 16 94,063,599 (GRCm39) missense probably benign 0.17
R2014:Hlcs UTSW 16 94,063,599 (GRCm39) missense probably benign 0.17
R2015:Hlcs UTSW 16 94,063,599 (GRCm39) missense probably benign 0.17
R2204:Hlcs UTSW 16 94,032,011 (GRCm39) missense probably benign 0.30
R2371:Hlcs UTSW 16 94,068,926 (GRCm39) missense probably damaging 0.98
R3816:Hlcs UTSW 16 93,933,947 (GRCm39) missense probably benign 0.11
R3822:Hlcs UTSW 16 94,068,840 (GRCm39) missense probably benign 0.04
R4422:Hlcs UTSW 16 93,939,819 (GRCm39) missense possibly damaging 0.56
R4657:Hlcs UTSW 16 94,063,557 (GRCm39) missense probably benign 0.00
R4783:Hlcs UTSW 16 94,069,398 (GRCm39) missense possibly damaging 0.82
R5347:Hlcs UTSW 16 94,068,383 (GRCm39) missense possibly damaging 0.93
R5808:Hlcs UTSW 16 94,063,491 (GRCm39) missense probably benign 0.00
R5940:Hlcs UTSW 16 93,935,571 (GRCm39) missense probably damaging 0.99
R6341:Hlcs UTSW 16 94,032,022 (GRCm39) missense probably damaging 1.00
R6943:Hlcs UTSW 16 93,942,261 (GRCm39) missense possibly damaging 0.75
R7053:Hlcs UTSW 16 94,068,874 (GRCm39) missense possibly damaging 0.91
R7157:Hlcs UTSW 16 94,069,023 (GRCm39) nonsense probably null
R7313:Hlcs UTSW 16 94,068,362 (GRCm39) missense probably damaging 1.00
R7427:Hlcs UTSW 16 94,068,758 (GRCm39) missense probably benign 0.00
R7428:Hlcs UTSW 16 94,068,758 (GRCm39) missense probably benign 0.00
R7547:Hlcs UTSW 16 94,032,031 (GRCm39) nonsense probably null
R7548:Hlcs UTSW 16 93,933,876 (GRCm39) nonsense probably null
R8172:Hlcs UTSW 16 94,068,485 (GRCm39) missense probably damaging 1.00
R8241:Hlcs UTSW 16 94,068,677 (GRCm39) missense probably damaging 1.00
R8500:Hlcs UTSW 16 94,063,617 (GRCm39) missense possibly damaging 0.89
R8940:Hlcs UTSW 16 94,032,085 (GRCm39) missense probably benign
R9274:Hlcs UTSW 16 94,088,785 (GRCm39) missense possibly damaging 0.85
R9360:Hlcs UTSW 16 93,932,672 (GRCm39) missense probably damaging 1.00
R9361:Hlcs UTSW 16 93,939,799 (GRCm39) missense probably benign 0.10
R9564:Hlcs UTSW 16 93,935,580 (GRCm39) missense probably benign 0.01
X0065:Hlcs UTSW 16 93,934,032 (GRCm39) missense probably damaging 1.00
Z1176:Hlcs UTSW 16 94,063,518 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGCTGTGGTTTTGAGGCACC -3'
(R):5'- CATTGTTTTAAGTGGCCCGTTC -3'

Sequencing Primer
(F):5'- TTTTGAGGCACCCACGG -3'
(R):5'- TAAGTGGCCCGTTCCAGTC -3'
Posted On 2019-06-26