Skip to main content
Have a personal or library account? Click to login
Monogenic Findings in Early Pregnancy Loss: Whole-Exome Sequencing Study of Euploid Products of Conception Cover

Monogenic Findings in Early Pregnancy Loss: Whole-Exome Sequencing Study of Euploid Products of Conception

Open Access
|May 2026

Figures & Tables

Figure 1.

Overview of molecular findings in 66 euploid early pregnancy losses. Diagnostic summary showing cases with a genetic diagnosis, possible monogenic contribution (VUS + P/VUS), and no reportable variant, with autosomal recessive (AR) and autosomal dominant (AD) findings indicated where applicable

Figure 2.

Overview of the identified genetic findings grouped by major developmental or organ-system association. (A) Genetic diagnoses, including definitive molecular diagnoses, and the pathogenic copy-number finding 21q22.12-q22.3 duplication. (B) Possible monogenic contributors. Genes are mapped to their principal affected systems, including neurologic, cardiac, blood/coagulation, kidney anomalies, skeletal, metabolic, ciliopathies, and multi-system involvement. CPLANE1 and RPGRIP1L are shown in both ciliopathy and multi-system categories because of their broader phenotypic effects.

Figure 3.

Pedigrees of families with definitive molecular diagnoses in the euploid early pregnancy loss cohort, grouped according to interpretive category. Previous losses, livebirths, and affected fetuses are shown for each family, and recurrent affected fetuses are integrated into the same pedigree when present.

Designed PCR primer sequences used in the confirmation and segregation analyses_

GeneVariantPrimer namePrimer nucleotide sequence (5′>3′)PCR length (nt)
CPLANE1c.1819delTCPLANE1_c.1819_FCCACCAATGAGTCTTGAGCTG732
CPLANE1_c.1819_RAAGAACGCCAAAGTGATGCTAT
c.7817T>ACPLANE1_c.7817_FTGGGTTTGTAGGAGGAGAGGT471
CPLANE1_c.7817_RCATACTTCCTGCTCCTTTTCCT
c.5820+3_5820+6delCPLANE1_c.5820_FGCCACACAGCATGGCTATATT431
CPLANE1_c.5820_RTCTCAAGGCTCATCTGGGAT
DHCR7c.452G>ADHCR7_c.452_FGTGAAGCAAGTTCCATCCCC586
DHCR7_c.452_RGCAGAACCAAAGGATGGACTC
c.964-1G>CDHCR7_c.964-1_FGCAGAACACGCTCTTGACAG721
DHCR7_c.964-1_RCAGGTAGAAGGCAGGTAGAGTT
RBM8Ac.-21G>ARBM8A_ex1_FTGAAGGGGGCGGAATCTCTA353
RBM8A_ex1_RTGCGTGTTTTTACCGTGCAG
NF1c.4537C>TNF1_ex35_FTGGTCCTGAGGTCTTTTTGG560
NF1_ex35_RTGTTGTCTTCACTCCCTGGT
F5c.1601G>AFV-Leiden_FTGATGCCCAGTGCTTAACAA265
FV-Leiden_RTCACACTGGTGCTAAAAAGGA
TSC1c.3113_3119delTSC1_ex23_FGGCTCTCAGAAAGGCTACTGG436
TSC1_ex23_RCATCCTCCGAATGTGGACAG
VWFc.3797C>TVWF_ex28_FACCGGGATCACAATGACCTT632
VWF_ex28_RGTAGGGCTCAGAAGTGTCCA
SLC6A1c.740C>ASLC6A1_ex8_FAAATGTGAGCTGGTTGGCTC432
SLC6A1_ex8_RAAACCTGGTCTACAGTGAGGG
DSG2c.2315delDSG2_ex14_FGCCCACTTGACTCAGATCCT590
DSG2_ex14_RTGGGTCCCATTTCTCTTTCCTTA
DVL1c.1961dupDLV1_ex15_FGGTTGTTCTGGACGTGGC722
DLV1_ex15_RGGTCTTCCTCATCCCAGGAG
RPGRIP1Lc.2771G>ARPGRIP1L_2771G_A_FGGGGTGGCAGCTTAGTTCTT389
RPGRIP1L_2771G_A_RCCTGGCTAGTTCACATGGTAG
c.3295-2A>GRPGRIP1L_3295-2_FAGGCCAATGGGCTTCTTTTCT3211
RPGRIP1L_3295-2_RGATGGTGATGTCATCGGCTG
RPGRIP1L_3295-2_seqGCAGAGGTGGGCGGATCATGAG
PAHc.842C>TPAH_ex7_FGCCAGCAATGAACCCAAACC239
PAH_ex7_RTCTTTTCATCCCAGCTTGCAC
c.*19G>TPAH_ex13_FACAAGTGGCCCATTTTGATGGT402
PAH_ex13_RGGCCCATTTTGATGGTGTTTT
GBAc.1444G>TGBA_ex10_FCTGCCTCTCCCACATGTGA391
GBA_ex10_RCAAAAGGGGATGGGTGTGC
c.1226A>GGBA_EX9_FCTTTTCTGCATCGCAGTCCA459
GBA_EX9_RTCCCACATGTGACCCTTACC
PKHD1c.107C>TPKHD1_ex3_FCAGGCCCACTTTTACACCTG423
PKHD1_ex3_RGGGGCTTCTGATGATGTGTTT
c.10883C>TPKHD1_ex61_FATCAGCCCTCATTTGGATGTGA537
PKHD1_ex61_RTTCCATTCACTTGGCCCTCA
PRDM6c.1057G>APRDM6_ex5_FATTGGTTGCTGGGGACAATC380
PRDM6_ex5_RAGTGAACCACGTTTCATGAGT
TBX18c.1570C>TTBX18_ex8_FGCAACTGGATGAAACAGGGG1074
TBX18_ex8_RCTCCAACCCTTGCCTTGTAAC
SCN5Ac.3911C>TSCN5A_ex22_FCACGGCCATAGGACATCAGA268
SCN5A_ex22_RTGTTCCCATCCTCCCCATTT
MYH3c.3137G>AMYH3_ex25_FTCTTCTGAAACTGGAGGCCC345
MYH3_ex25_RCTTGCAAAGCATTTGTTCCCA

Zygosity, inheritance, OMIM-associated diseases, and interpretive grouping of the detected genes

CaseGeneVariantAccession numberAF (gnomAD)Internal frequencyOMIM disease/s; InheritanceMajor developmental / organ system
1. Genes plausibly associated with prenatal or early embryonic lethality
Definitive molecular diagnoses
Abp-411CPLANE1c.1819delT;7817T>Ars777686211; rs7495237550.0001554; 0.000023900.0077614615, Joubert Syndrome 17, AR; 277170, Orofaciodigital syndrome VI, ARMulti-system
Abp-4451CPLANE1c.1819delT;7817T>Ars777686211; rs7495237550.0001554; 0.000023900.0077614615, Joubert Syndrome 17, AR; 277170, Orofaciodigital syndrome VI, ARMulti-system
c.5820+3_5820+6del//0.0017
Abp-4942DHCR7c.452G>Ars115552170.00077590.0084270400, Smith-Lemli-Opitz syndrome, ARMulti-system
c.964-1G>Crs1386591670.0038540.0042
Abp-5452DHCR7c.452G>Ars115552170.00077590.0084270400, Smith-Lemli-Opitz syndrome, ARMulti-system
c.964-1G>Crs1386591670.0038540.0042
Abp-5511CPLANE1c.1819delT;7817T>Ars777686211; rs7495237550.0001554; 0.000023900.0077614615, Joubert Syndrome 17, AR; 277170, Orofaciodigital syndrome VI, ARMulti-system
c.5820+3_5820+6del//0.0017
Possible monogenic contributors
Abp-501GBA1c.1444G>T//0608013, 230800, 230900, 231000, 231005, Gaucher disease types perinatal death, I, II, III, IIIC, ARMulti-system
c.1226A>Grs767637150.0022350.0067
Abp-694PKHD1c.107C>Trs1378529440.00050940.0014263200, Polycystic kidney disease 4, with or without hepatic disease, ARKidney anomalies
c.10883C>Trs1477006430.000053120
Abp-825RPGRIP1Lc.2771G>Ars142234650/0611561, Meckel syndrome 5, AR; 611560, Joubert syndrome 7, ARCiliopathies/multi-system
c.3295-2A>Grs1258182460/0
2. Genes causing severe congenital disorders not typically considered embryonically lethal
Definitive molecular diagnoses
Abp-251SLC6A1c.740C>A//0616421, Myoclonic-atonic epilepsy, ADNeurologic
Abp-716RBM8Ac.-21G>Ars1394282920.01794>2%274000, Thrombocytopenia-absent radius syndrome, ARMulti-system
1q21.1-q21.2chr1:143,767,833-149,400,542//0
Abp-799NF1c.4600C>Trs7607035050.0000079570162200, Neurofibromatosis, type 1, ADMulti-system
Abp-801DSG2c.2315del//0610193, Arrhythmogenic right ventricular dysplasia 10, ADCardiac
Abp-825DVL1c.1961dup//0616331, Robinow syndrome, autosomal dominant 2, ADSkeletal
Possible monogenic contributors
Abp-80PAHc.842C>Trs50308510.00010260.0010261600, Phenylketonuria, ARMetabolic
c.*19G>Trs3726370210.0020290
Abp-87PRDM6c.1057G>Ars2022247620.00026040.0010617039, Patent ductus arteriosus 3, ADCardiac
Abp-166TBX18c.1570C>Trs7609055890.0000080610.0010143400, Congenital anomalies of kidney and urinary tract 2, ADKidney anomalies
Abp-233SCN5Ac.3911C>Trs1994736030.00016490601144, Brugada syndrome 1, AD; 601154, Cardiomyopathy, dilated, 1E, AD; 603830, Long QT syndrome 3, ADCardiac
Abp-577TSC1c.3113_3119del//0.00035191100, Tuberous sclerosis-1, ADMulti-system
Abp-781MYH3c.3137G>Ars1420024490.00040310.0010193700, Arthrogryposis, distal, type 2A (Freeman-Sheldon), ADSkeletal
3. Genes linked to later-onset or susceptibility phenotypes
Abp-668VWFc.3797C>Trs617493700.00083220.0010193400, von Willebrand disease, AD/ARBlood
Abp-809F5c.1601G>Ars60250.01752>3%188055, Thrombophilia 2 due to activated protein C resistance, AD; 614389, {Pregnancy loss, recurrent, susceptibility to, 1}, ADBlood
Additional distinct pathogenic copy-number finding
Abp-972 [U]21q22.12-q22.3chr21:33,398,108–43,587,648//0/, 21q22 Duplication SyndromeMulti-system

Detailed overview of variants detected by WES in euploid EPL and their molecular characteristics

CaseGeneReference sequenceVariantProtein changeZygosityInheritanceType of variantKnown / NovelACMG classificationACMG criteria
1. Genes plausibly associated with prenatal or early embryonic lethality
Definitive molecular diagnoses
Abp-411CPLANE1NM_001384732.1c.1819delT;7817T>Ap.Tyr607ThrfsTer6; p.Leu2624TerhomM/FFrameshiftKnownPathogenicPVS1; PM2; PP5/PVS1; PM2; PP5
Abp-445 1CPLANE1NM_001384732.1c.1819delT;7817T>Ap.Tyr607ThrfsTer6; p.Leu2624TerhetFFrameshift; NonsenseKnownPathogenicPVS1; PM2; PP5/PVS1; PM2; PP5
c.5820+3_5820+6delexon 29 skippinghetMSplice siteNovelPathogenicPS3, PM2; PM3; PM4; PP3
Abp-4942DHCR7NM_001360.3c.452G>Ap.Trp151TerhetFNonsenseKnownPathogenicPVS1; PM2; PP5
c.964-1G>Caltered splicinghetMSplice siteKnownPathogenicPVS1; PM2; PP5
Abp-5452DHCR7NM_001360.3c.452G>Ap.Trp151TerhetFNonsenseKnownPathogenicPVS1; PM2; PP5
c.964-1G>Caltered splicinghetMSplice siteKnownPathogenicPVS1; PM2; PP5
Abp-5511CPLANE1NM_001384732.1c.1819delT;7817T>Ap.Tyr607ThrfsTer6; p.Leu2624TerhetFFrameshift; NonsenseKnownPathogenicPVS1; PM2; PP5/PVS1; PM2; PP5
c.5820+3_5820+6delexon 29 skippinghetMSplice siteNovelPathogenicPVS1; PM2; PP5/PVS1; PM2; PP5
Possible monogenic contributors
Abp-501GBA1NM_000157.4c.1444G>Tp.Asp482TyrhetMMissenseKnownVUSPM2; PM3; PP3
c.1226A>Gp.Asn409SerhetFMissenseKnownLikely pathogenicPM1; PM2; PM5; PP2; PP3; PP5
Abp-694PKHD1NM_138694.4c.107C>Tp.Thr36MethetMMissenseKnownLikely pathogenicPM2; PM5; PP3; PP5
c.10883C>Tp.Thr362IlehetFMissenseKnownVUSPM2; PM3
Abp-825RPGRIP1LNM_015272.5c.2771G>Ap.Ser924AsnhetMMissenseKnownVUSPM2, PM3
c.3295-2A>G/hetFSplice siteKnownLikely pathogenicPVS1; PM2; PP5
2. Genes causing severe congenital disorders not typically considered embryonically lethal
Definitive molecular diagnoses
Abp-251SLC6A1NM_003042.4c.740C>Ap.Pro247Hishetde novoMissenseNovelLikely pathogenicPM2; PM5; PP2; PP3
Abp-716RBM8ANM_005105.5c.-21G>A/hetMMissense/noncodingKnownPathogenic, low penetrancePS3, PM3
1q21.1-q21.2hg19chr1:143,767,833-149,400,542/hetFDeletionKnownPathogenic2A; 3B; 4L >1 point
Abp-799NF1NM_001042492.3c.4600C>Tp.Arg1513TerhetFNonsenseKnownPathogenicPVS1; PM2; PP5
Abp-801DSG2NM_001943.5c.2315delp.Leu772TerhetMNonsenseNovelLikely pathogenicPVS1; PM2
Abp-825DVL1NM_001330311.2c.1961dupp.Pro657AlafsTer50hetFFrameshiftNovelLikely pathogenicPVS1; PM2
Possible monogenic contributors
Abp-80PAHNM_000277.3c.842C>Tp.Pro281LeuhetMMissenseKnownPathogenicPS3, PM2; PM5; PP2; PP3; PP5
c.*19G>T/hetFMissense/noncodingKnownVUSPM3; BS1; BS2; BP7
Abp-87PRDM6NM_001136239.4c.1057G>Ap.Asp353AsnhetMMissenseKnownVUSPM2
Abp-166TBX18NM_001080508.3c.1570C>Tp.His524TyrhetMMissenseKnownVUSPM2; PP3; PP5
Abp-233SCN5ANM_000335.5c.3911C>Tp.Thr1304MethetFMissenseKnownVUSPM2, PP3, PP5
Abp-577TSC1NM_000368.5c.3113_3119delp.Ser1038ThrfsTer51hetFFrameshiftNovelVUSPVS1(moderate); PM2
Abp-781MYH3NM_002470.4c.3137G>Ap.Arg1046GlnhetMMissenseKnownVUSPM2; PP3
3. Genes linked to later-onset or susceptibility phenotypes
Abp-668VWFNM_000552.5c.3797C>Tp.Pro1266LeuhetMMissenseKnownLikely pathogenicPM1; PM2; PM5; PP5
Abp-809F5NM_000130.5c.1601G>Ap.Arg534GlnhomM (hom)/F (het)MissenseKnownPathogenic, low penetrancePS3, PS4
Additional distinct pathogenic copy-number finding
Abp-97221q22.12-q22.3duphg19chr21:33,398,108-43,587,648/hetde novoDuplicationKnownPathogenic3C; 4L >1 point

Detailed overview of the demographic and clinical characteristics of the EPL studied group

Sample IDFetal sexEthnic originGestational age (weeks)Maternal AgeNo. of PLs (n)Livebirths (n)
1Abp-2FMKD84241
2Abp-26FALB73050
3Abp-76MMKD83130
4Abp-80FALB62660
5Abp-87MALB92941
6Abp-166FALB738120
7Abp-233FMKD84040
8Abp-251MMKD82940
9Abp-2581FMKD831110
10Abp-266FMKD73240
11Abp-2722MALB112840
12Abp-278FALB92442
13Abp-303FALB82920
14Abp-312MALB122731
15Abp-357MMKD94130
16Abp-367MALB83030
17Abp-3722MALB92960
18Abp-395MMKD92731
19Abp-404MALB72830
20Abp-407MALB83530
21Abp-411MALB83050
22Abp-4443FMKD92720
23Abp-4454FALB102420
24Abp-4575MALB92730
25Abp-488MALB83431
26Abp-494MMKD73230
27Abp-501FALB83170
28Abp-5176FALB82510
29Abp-5514FALB82530
30Abp-562MALB63230
31Abp-577FMKD84131
32Abp-5897FMKD83620
33Abp-5901MMKD835130
34Abp-591FMKD83540
35Abp-6013FMKD82830
36Abp-604MALB92940
37Abp-642FALB92530
38Abp-6565MALB72940
39Abp-6657MMKD73730
40Abp-666MMKD73340
41Abp-668MMKD103720
42Abp-677FMKD83140
43Abp-682FALB92620
44Abp-694MALB92320
45Abp-699MMKD122920
46Abp-715FALB82640
47Abp-716FMKD93120
48Abp-722MMKD63430
49Abp-729FMKD83620
50Abp-734MALB72431
51Abp-741MALB92230
52Abp-746MMKD83221
53Abp-781FMKD93320
54Abp-786FALB82720
55Abp-799MMKD83541
56Abp-801FMKD82521
57Abp-809MALB122030
58Abp-812FMKD63631
59Abp-8136MALB83030
60Abp-825FMKD73731
61Abp-833FMKD73920
62Abp-859MALB83123
63Abp-864MALB92430
64Abp-866FMKD84231
65Abp-900MMKD83720
66Abp-972FALB93141

PCR mixture and cycling conditions used for Sanger sequencing for confirmation and phasing of the detected variants on WES analysis_

PCR master mix content:Volume (ul)
H2O16.1
10xB2 buffer2.5
25mM MgCl21.3
2.5 mM nucleotide mix2
10mM Forward primer1
10 mM Reverse primer1
HotFire Polymerase 1U/ul0.1
DNA (100ng/ul)1
Total volume:25
PCR cycling conditions:
95°C/15 minx1 cycle
95°C/30 secx33 cycles
59°C/30 sec
72°C/45 sec
72°C/10 minx1 cycle
Language: English
Page range: 5 - 20
Published on: May 14, 2026
In partnership with: Paradigm Publishing Services
Publication frequency: 2 issues per year

© 2026 Gj Bozhinovski, P Noveski, M Terzikj, K Kubelka-Sabit, D Plaseska-Karanfilska, published by Macedonian Academy of Sciences and Arts
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.