Phenotypic Mutation 'lilliputian3' (pdf version)
Allelelilliputian3
Mutation Type splice site
Chromosome1
Coordinate158,609,973 bp (GRCm39)
Base Change A ⇒ T (forward strand)
Gene Pappa2
Gene Name pappalysin 2
Synonym(s) PAPP-A2, placenta-specific 3, pregnancy-associated plasma preproprotein-A2, pregnancy-associated plasma protein-E, PLAC3, Pappe
Chromosomal Location 158,539,297-158,788,019 bp (-) (GRCm39)
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 pappalysin family of metzincin metalloproteinases. The encoded protein cleaves insulin-like growth factor-binding protein 5 and is thought to be a local regulator of insulin-like growth factor (IGF) bioavailability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]
PHENOTYPE: Mice homozygous for a null mutation are viable and fertile but display postnatal growth retardation that is more pronounced in females compared to males. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_001085376; MGI:3051647

MappedYes 
Amino Acid Change
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000124022 ]   † probably from a misspliced transcript
AlphaFold E9PZ87
SMART Domains Protein: ENSMUSP00000124022
Gene: ENSMUSG00000073530

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Pfam:Laminin_G_3 271 440 1.2e-25 PFAM
NL 572 614 2.81e-5 SMART
Pfam:Peptidase_M43 669 832 1.5e-12 PFAM
Blast:FN3 844 1103 1e-169 BLAST
low complexity region 1130 1139 N/A INTRINSIC
low complexity region 1361 1370 N/A INTRINSIC
CCP 1394 1457 4.97e0 SMART
CCP 1462 1519 4.81e-1 SMART
CCP 1523 1588 2.58e-4 SMART
CCP 1593 1644 1.13e0 SMART
NL 1720 1757 2.66e-6 SMART
Predicted Effect probably null
SMART Domains Protein: ENSMUSP00000124022
Gene: ENSMUSG00000073530

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Pfam:Laminin_G_3 271 440 1.2e-25 PFAM
NL 572 614 2.81e-5 SMART
Pfam:Peptidase_M43 669 832 1.5e-12 PFAM
Blast:FN3 844 1103 1e-169 BLAST
low complexity region 1130 1139 N/A INTRINSIC
low complexity region 1361 1370 N/A INTRINSIC
CCP 1394 1457 4.97e0 SMART
CCP 1462 1519 4.81e-1 SMART
CCP 1523 1588 2.58e-4 SMART
CCP 1593 1644 1.13e0 SMART
NL 1720 1757 2.66e-6 SMART
Predicted Effect probably null
SMART Domains Protein: ENSMUSP00000124022
Gene: ENSMUSG00000073530

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Pfam:Laminin_G_3 271 440 1.2e-25 PFAM
NL 572 614 2.81e-5 SMART
Pfam:Peptidase_M43 669 832 1.5e-12 PFAM
Blast:FN3 844 1103 1e-169 BLAST
low complexity region 1130 1139 N/A INTRINSIC
low complexity region 1361 1370 N/A INTRINSIC
CCP 1394 1457 4.97e0 SMART
CCP 1462 1519 4.81e-1 SMART
CCP 1523 1588 2.58e-4 SMART
CCP 1593 1644 1.13e0 SMART
NL 1720 1757 2.66e-6 SMART
Predicted Effect probably null
SMART Domains Protein: ENSMUSP00000124316
Gene: ENSMUSG00000073530

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
CCP 67 130 4.97e0 SMART
CCP 135 192 4.81e-1 SMART
CCP 196 245 2.84e0 SMART
Predicted Effect probably null
SMART Domains Protein: ENSMUSP00000124316
Gene: ENSMUSG00000073530

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
CCP 67 130 4.97e0 SMART
CCP 135 192 4.81e-1 SMART
CCP 196 245 2.84e0 SMART
Predicted Effect probably null
SMART Domains Protein: ENSMUSP00000124316
Gene: ENSMUSG00000073530

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
CCP 67 130 4.97e0 SMART
CCP 135 192 4.81e-1 SMART
CCP 196 245 2.84e0 SMART
Predicted Effect probably null
Meta Mutation Damage Score 0.9755 question?
Is this an essential gene? Non Essential (E-score: 0.000) question?
Phenotypic Category Autosomal Recessive
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance  
Alleles Listed at MGI

All Mutations and Alleles(6) : Chemically induced (other)(2) Targeted(4)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01097:Pappa2 APN 1 158684718 missense probably damaging 1.00
IGL01394:Pappa2 APN 1 158592674 splice site probably benign
IGL01570:Pappa2 APN 1 158642110 nonsense probably null
IGL01618:Pappa2 APN 1 158684948 missense probably damaging 1.00
IGL01717:Pappa2 APN 1 158684702 critical splice donor site probably null
IGL01804:Pappa2 APN 1 158764089 missense probably benign
IGL01904:Pappa2 APN 1 158611511 missense probably damaging 0.99
IGL02116:Pappa2 APN 1 158672695 missense probably benign 0.01
IGL02174:Pappa2 APN 1 158589188 missense probably damaging 1.00
IGL02302:Pappa2 APN 1 158542571 missense probably benign 0.38
IGL02422:Pappa2 APN 1 158764503 missense probably damaging 1.00
IGL02572:Pappa2 APN 1 158678786 missense probably benign
IGL02659:Pappa2 APN 1 158764364 missense probably damaging 0.97
IGL02887:Pappa2 APN 1 158609829 missense probably damaging 1.00
IGL02981:Pappa2 APN 1 158678714 missense probably benign 0.00
IGL03128:Pappa2 APN 1 158764054 missense probably benign 0.16
IGL03142:Pappa2 APN 1 158682501 missense probably damaging 1.00
IGL03270:Pappa2 APN 1 158592637 missense possibly damaging 0.78
Fritas UTSW 1 158675533 missense possibly damaging 0.77
Gulliver UTSW 1 158684706 missense probably null 1.00
Lilliputian UTSW 1 158544560 missense probably damaging 1.00
Lilliputian2 UTSW 1 158662488 nonsense probably null
Pitzel UTSW 1 158784215 missense probably damaging 1.00
shrink UTSW 1 158590762 missense probably damaging 1.00
R0106:Pappa2 UTSW 1 158542547 missense probably damaging 1.00
R0106:Pappa2 UTSW 1 158542547 missense probably damaging 1.00
R0172:Pappa2 UTSW 1 158682419 critical splice donor site probably null
R0194:Pappa2 UTSW 1 158592671 splice site probably benign
R0418:Pappa2 UTSW 1 158544560 missense probably damaging 1.00
R0421:Pappa2 UTSW 1 158675650 missense probably damaging 1.00
R0441:Pappa2 UTSW 1 158590628 unclassified probably benign
R0602:Pappa2 UTSW 1 158590625 unclassified probably benign
R0630:Pappa2 UTSW 1 158660343 missense probably benign
R0760:Pappa2 UTSW 1 158544531 critical splice donor site probably null
R1146:Pappa2 UTSW 1 158682552 missense probably damaging 1.00
R1146:Pappa2 UTSW 1 158682552 missense probably damaging 1.00
R1243:Pappa2 UTSW 1 158672670 missense probably damaging 1.00
R1413:Pappa2 UTSW 1 158764124 missense probably benign 0.00
R1502:Pappa2 UTSW 1 158784858 missense probably damaging 1.00
R1599:Pappa2 UTSW 1 158684742 missense probably damaging 1.00
R1689:Pappa2 UTSW 1 158784968 missense probably damaging 1.00
R1750:Pappa2 UTSW 1 158590720 nonsense probably null
R1772:Pappa2 UTSW 1 158641938 missense possibly damaging 0.92
R1832:Pappa2 UTSW 1 158684886 missense probably damaging 1.00
R1905:Pappa2 UTSW 1 158631073 splice site probably null
R1914:Pappa2 UTSW 1 158578133 missense probably damaging 0.97
R2013:Pappa2 UTSW 1 158662498 missense probably damaging 1.00
R2037:Pappa2 UTSW 1 158784214 nonsense probably null
R2118:Pappa2 UTSW 1 158684836 missense probably damaging 1.00
R2268:Pappa2 UTSW 1 158684841 missense probably damaging 1.00
R2269:Pappa2 UTSW 1 158684841 missense probably damaging 1.00
R2347:Pappa2 UTSW 1 158592613 missense probably damaging 1.00
R3024:Pappa2 UTSW 1 158763795 missense probably benign 0.00
R3706:Pappa2 UTSW 1 158662488 nonsense probably null
R3707:Pappa2 UTSW 1 158662488 nonsense probably null
R3708:Pappa2 UTSW 1 158662488 nonsense probably null
R4600:Pappa2 UTSW 1 158642015 missense probably damaging 1.00
R4737:Pappa2 UTSW 1 158784582 missense probably benign
R4738:Pappa2 UTSW 1 158784582 missense probably benign
R4739:Pappa2 UTSW 1 158784572 missense probably damaging 0.99
R4739:Pappa2 UTSW 1 158784582 missense probably benign
R4788:Pappa2 UTSW 1 158611487 missense possibly damaging 0.86
R4798:Pappa2 UTSW 1 158684949 missense probably damaging 0.99
R4952:Pappa2 UTSW 1 158684706 missense probably null 1.00
R5121:Pappa2 UTSW 1 158666197 missense probably benign 0.01
R5144:Pappa2 UTSW 1 158784703 missense probably benign 0.03
R5159:Pappa2 UTSW 1 158589189 missense probably damaging 1.00
R5278:Pappa2 UTSW 1 158609973 splice site probably null
R5428:Pappa2 UTSW 1 158642355 missense possibly damaging 0.53
R5452:Pappa2 UTSW 1 158666172 missense probably benign 0.00
R5477:Pappa2 UTSW 1 158784308 missense probably benign 0.00
R5504:Pappa2 UTSW 1 158675615 missense probably benign 0.00
R5852:Pappa2 UTSW 1 158544584 missense probably damaging 1.00
R6003:Pappa2 UTSW 1 158763820 missense probably benign 0.23
R6129:Pappa2 UTSW 1 158542567 nonsense probably null
R6137:Pappa2 UTSW 1 158699113 missense probably damaging 1.00
R6374:Pappa2 UTSW 1 158784215 missense probably damaging 1.00
R6472:Pappa2 UTSW 1 158662369 missense probably damaging 1.00
R6804:Pappa2 UTSW 1 158764438 missense probably benign 0.24
R7020:Pappa2 UTSW 1 158675579 missense probably damaging 0.98
R7051:Pappa2 UTSW 1 158784753 missense unknown
R7082:Pappa2 UTSW 1 158590689 missense possibly damaging 0.65
R7111:Pappa2 UTSW 1 158784096 missense probably benign 0.38
R7213:Pappa2 UTSW 1 158764456 missense possibly damaging 0.93
R7575:Pappa2 UTSW 1 158642100 missense probably damaging 1.00
R7587:Pappa2 UTSW 1 158678701 missense probably damaging 1.00
R7826:Pappa2 UTSW 1 158764010 nonsense probably null
R7957:Pappa2 UTSW 1 158589131 nonsense probably null
R8007:Pappa2 UTSW 1 158609874 missense probably damaging 0.99
R8050:Pappa2 UTSW 1 158675970 missense probably damaging 1.00
R8063:Pappa2 UTSW 1 158764126 missense possibly damaging 0.79
R8068:Pappa2 UTSW 1 158763555 missense possibly damaging 0.87
R8128:Pappa2 UTSW 1 158764234 missense possibly damaging 0.75
R8264:Pappa2 UTSW 1 158682543 missense probably damaging 1.00
R8317:Pappa2 UTSW 1 158592530 missense probably damaging 1.00
R8499:Pappa2 UTSW 1 158764092 missense probably damaging 1.00
R8744:Pappa2 UTSW 1 158611487 missense possibly damaging 0.86
R8793:Pappa2 UTSW 1 158678731 missense probably damaging 1.00
R8932:Pappa2 UTSW 1 158590762 missense probably damaging 1.00
R9004:Pappa2 UTSW 1 158764518 missense possibly damaging 0.67
R9004:Pappa2 UTSW 1 158763979 missense probably damaging 1.00
R9088:Pappa2 UTSW 1 158763927 missense probably damaging 1.00
R9191:Pappa2 UTSW 1 158684988 missense probably damaging 1.00
R9243:Pappa2 UTSW 1 158763763 missense probably damaging 0.99
R9280:Pappa2 UTSW 1 158675533 missense possibly damaging 0.77
R9301:Pappa2 UTSW 1 158672614 missense probably damaging 0.96
R9306:Pappa2 UTSW 1 158764492 missense probably damaging 1.00
R9367:Pappa2 UTSW 1 158784542 missense probably benign 0.40
R9471:Pappa2 UTSW 1 158642029 missense probably benign 0.04
R9544:Pappa2 UTSW 1 158784817 missense probably damaging 0.99
R9680:Pappa2 UTSW 1 158609818 missense possibly damaging 0.78
R9762:Pappa2 UTSW 1 158684948 missense probably damaging 1.00
R9774:Pappa2 UTSW 1 158675920 missense probably damaging 0.99
R9776:Pappa2 UTSW 1 158611481 missense probably damaging 1.00
X0058:Pappa2 UTSW 1 158641967 missense probably null
X0061:Pappa2 UTSW 1 158764188 missense possibly damaging 0.87
Z1176:Pappa2 UTSW 1 158784503 missense probably benign
Z1176:Pappa2 UTSW 1 158642386 missense probably damaging 1.00
Z1176:Pappa2 UTSW 1 158642384 missense probably damaging 1.00
Mode of Inheritance Autosomal Recessive
Local Stock
Repository
Last Updated 2019-09-04 9:38 PM by Diantha La Vine
Record Created 2017-09-11 10:26 AM
Record Posted 2017-09-15
Phenotypic Description
Figure 1. Lilliputianmice exhibit reduced body weights compared to wild-type littermates. Scaled body weight data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

The lilliputian3 phenotype was identified among G3 mice of the pedigree R5278, some of which showed reduced body weights compared to wild-type littermates (Figure 1).

Nature of Mutation
Figure 2. Linkage mapping of the reduced body weight using a recessive model of inheritance. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 53 mutations (X-axis) identified in the G1 male of pedigree R5278. Scaled body weight phenotype data are shown for single locus linkage analysis without consideration of G2 dam identity.  Horizontal pink and red lines represent thresholds of P = 0.05, and the threshold for P = 0.05 after applying Bonferroni correction, respectively.

Whole exome HiSeq sequencing of the G1 grandsire identified 53 mutations. The body weight phenotype was linked to a mutation in Pappa2: a T to A transversion at base pair 158,782,403 (v38) on chromosome 1, or base pair 198,125 in the GenBank genomic region NC_000067 within intron 15 (nine base pairs from exon 16). Linkage was found with a recessive model of inheritance (P = 0.000255), wherein two variant homozygotes departed phenotypically from 24 homozygous reference mice and 21 heterozygous mice (Figure 2).

The effect of the mutation at the cDNA and protein levels has not been examined, but the mutation is predicted to result in the use of a cryptic site in intron 15. The resulting transcript would have a 7-base pair insertion of intron 15, which would cause a frame-shifted protein product beginning after amino acid 1,499 of the protein and premature termination after the inclusion of 10 aberrant amino acids.

C57BL/6J:

         <--exon 14      <--exon 15     <--intron 15 exon 16-->        <--exon 22
4306 ……AGGAACATGCAG ……GCTAAGCTCCAAG ……ttttctggagtcag GACTGAACCCA…… ……GAAAACCAGTAA…… 5370
1436 ……-R--N--M--Q- ……-A--K--L--Q--                  G--L--N--P-…… ……-E--N--Q--*-   1789
      

The acceptor splice site of intron 15, which is destroyed by the lilliputian3 mutation, is indicated in blue lettering and the mutated nucleotide is indicated in red. 

Illustration of Mutations in
Gene & Protein
Protein Prediction
Figure 3. Domain figure of PAPP-A2. The lilliputian3 mutation occurs with intron 15. Abbreviations: SP, signal peptide; Laminin, laminin G-like domain; LNR, Lin12/Notch repeats; FN3, fibronectin 3-like domain; CCP/SCR, complement control protein/short consensus repeat. This image is interactive. Other mutations found in PAPP-A2 are noted. Click on each mutation for more information.

Pappa2 encodes pregnancy-associated plasma protein A2 (PAPP-A2; alternatively, PAPP-E), a member of the pappalysin group of the metzincin protease family along with PAPP-A and ulilysin. PAPP-A2 is a 1,789-amino acid protein that has several domains: a signaling peptide (amino acids 1-18), a laminin G-like domain (amino acids 271-440), a peptidase/proteolytic domain (amino acids 669-832), a fibronectin 3-like domain (FN3; amino acids 844-1103), four complement control protein (CCP) domains (alternatively, short consensus repeat (SCR); amino acids 1394-1457, 1462-1519, 1523-1588, and 1593-1644), and two Lin12/Notch repeats (LNRs; amino acids 572-614 and 1720-1757) (Figure 3) (1).

The mutation in lilliputian3 results in frame-shifted protein product beginning after amino acid 1,499 of the protein and premature termination after the inclusion of 10 aberrant amino acids. Amino acid 1,499 is within the second CCP domain.

Please see the record Lilliputian for more information about Pappa2.

Putative Mechanism

PAPP-A2 is a protease that acts on insulin-like growth factor binding protein 5 (IGFBP5), a factor involved in bone metabolism (2;3) and IGFBP3 (4). IGFBP5 regulates the IGF-I signaling pathways by binding IGF-I. IGFBP5 also has IGF-I-independent functions. IGFPB5 is able to bind its putative receptor to enter the cytoplasm and subsequently interact with, and regulate, other proteins. Studies have shown that PAPP-A2 has roles in human pregnancy (5), reproductive traits in cattle (6), and postnatal growth in mice (7;8). Pappa2-deficient (Pappa2-/-) mice are viable and smaller than wild-type mice (8). At 3-18 weeks of age, the male Pappa2-/- mice had approximately 10% lower body weights than that in age-matched wild-type mice (8). Weight reduction was more pronounced in female mice compared to that in age-matched male mice (8). In the female mice, all organs except ovaries were larger than that in wild-type mice. The Pappa2-/- mice have shorter femur length than that in wild-type mice, but do not exhibit changes in bone mineral density. Pappa2 deletion does not affect placental or embryonic mass at embryonic day 12.5 (9). At birth, the Pappa2-/- mice exhibited a trend towards lower birth mass (9). At 3, 6, and 10 weeks of age, the Pappa2-/- mice exhibited reduced body mass and tail lengths compared to wild-type mice (9). The shape of the pelvic girdle significantly differed between that in the Pappa2-/- and wild-type mice; the Pappa2-/- mice had a more feminine shape and was disproportionately small (9). Matings between Pappa2-/- mice exhibited a delay to first litter, increased number of days between litter, and a reduced number of pups per litter compared to matings between wild-type mice (8). Although Pappa2 deletion results in diminished levels of circulating IGF-I, IGFBP-3, and IGFBP-5, there were no glucose metabolism phenotypes observed (10). In addition, loss of Pappa2 expression did not result in weight gain or adiposity on a high-fat diet (10). Loss of Pappa2 expression in mouse does not effect female fertility, but has subtle effects on male fertility (11). The body weight phenotype of the lilliputian3 mice indicates loss-of-function of PAPP-A2lilliputian3.

Primers PCR Primer
lilliputian3_pcr_F: ACAGGAACACTCACTTCTTGC
lilliputian3_pcr_R: ACCTCACTGAGAACTGTAGAGTAAG

Sequencing Primer
lilliputian3_seq_F: ACATAGTAGCCTGGTTTGCAC
lilliputian3_seq_R: TCCACATAGGAGGGAGAT
Genotyping

PCR program

1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40x
6) 72°C 10:00
7) 4°C hold


The following sequence of 413 nucleotides is amplified (chromosome 1, - strand):


1   acctcactga gaactgtaga gtaagtactt ataggatcca cataggaggg agattttaga
61  gacgctactc aacaaagaat aaggggactt aaagagagcc agtataggca tagtttttgg
121 ttccttgtgc tgttgtcatg agctcgctgt tctgagcacc atgtaattct cttttctgga
181 gtcaggactg aacccatggc tgacatgtct tgaagatgga ctctggtctc tccctgaagt
241 ctactgcaag ttggaatgtg aagctcctcc agttattccc aatgccaatc tgctcctgcc
301 acatttcctg gaaggcaacc atgatgtggg caccatctgc aaatatgagt gcaaaccagg
361 ctactatgtg aaggagactt caggaagtca aggcaagaag tgagtgttcc tgt


Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.

References
Science Writers Anne Murray
Illustrators Diantha La Vine
AuthorsEmre Turer and Bruce Beutler