Table SI. Different forms of congenital and associated causative selected in the present study. RefSeq RefSeq (genome) (mRNA) CDS Number alteration Full name function symbol accession accession length of exons number number A thyroid enriched Paired box gene NG_012384 factor, involved in thyroid follicular PAX8 NM_003466 1353 12 eight .1 cell development and expression of thyroid-specific genes. Thyroid FOXE1 NG_011979 NM_004473. A functions in transcription 1122 1 （TTF-2） .1 3 thyroid development factor 2 NK2 transcription Thyroid NG_013340 NM_004387. A transcription factor functions in NKX2-5 factor related, locus 975 2 dysgenesis .1 3 heart formation and development 5 A for thyrothropin and Thyroid stimulating NG_009206 NM_000369. TSHR 2295 10 thyrostimulin, a major controller of .1 2 Primary thyroid cell metabolism congenital A thyroid-specific transcription hypothyro NKX2-1 NG_013365 factor，regulates the expression of NK2 1 NM_0010796 1206 3 idism (TTF-1) .1 thyroid-specific genes and genes 68.2 involved in morphogenesis DUOX2 NG_009447 NM_014080. Dual oxidase 2 4647 34 H O generation in the follicle （THOX2) .1 4 2 2 Necessary for proper cellular Dual oxidase NG_016992 NM_207581. DUOXA2 963 6 localization and maturation of maturation factor 2 .1 3 functional dual oxidase 2. Dysormonogenesis Catalyses the oxidation, NG_011581 NM_000547. TPO 2802 17 organification, and coupling .1 5 reactions Solute carrier family SLC26A4( NG_008489 NM_000441. Transports iodine across apical 26, member 4 2343 21 PDS) .1 1 membrane (Pendred syndrome, PDS

NG_015832 NM_003235. Supports for thyroid hormone TG Thyroglobulin 8307 48 .1 4 synthesis Solute carrier family SLC5A5(N 5 (sodium iodide NG_012930 NM_000453. Transports iodine across basal 1932 15 IS) symporter), member .1 2 membrane 5 : Nitroreductase-related IYD Iodotyrosine NM_203395. NG_016007 870 5 capable of deiodinating (DEHAL1) deiodinase 2 .1 iodotyrosines Essential bound protein mediating SECIS binding NG_012177 NM_024077. SECISBP2 2565 17 the correct binding of selenium with protein 2 .1 3 thyroxine deiodinated enzyme

The beta subunit of thyroid (Aliases: TSH-B, NG_015891 NM_000549. stimulating hormone, functions in TSHB TSH-BETA) 417 3 .1 3 the control of thyroid structure and Isolated central Thyroid stimulating metabolism congenital hormone beta hypothyroidism(is May be involved in the expression Immunoglobulin olated TSH NG_021190 NM_0011709 of normal TRHR expression, IGSF1 superfamily, 4026 20 deficiency) .1 61.1 causative gene of X-linked central Secondary member 1 hypothyroidism or Central Thyrotropin-releasin NG_017161 NM_003301. AG protein-coupled receptor for hypothyro TRHR 1197 2 g hormone receptor .1 5 thyrotropin-releasing hormone idism Homeobox gene A transcriptional repressor in the NG_008242 NM_003865. Combined HESX1 expressed in ES 558 4 developing forebrain and pituitary .1 2 pituitary hormone cells gland deficiencies(Defici A transcription factor that is LIM homeobox NG_008097 NM_014564. ency in pituitary LHX3 1209 6 required for pituitary development protein 3 .1 3 transcription and motor neuron specification factors) LIM homeobox NG_008081 NM_033343. A transcription factor involved in LHX4 1173 6 protein 4 .1 3 the control of differentiation and development of the pituitary gland

Regulates the expression of several POU domain, class POU1F1 NM_000306. genes involved in pituitary 1, transcription NG_008225 876 6 （PIT1） 2 development and hormone factor 1 .2 expression. Prophet of Pit1, paired-like NG_015889 NM_006261. A transcription factor responsible PROP1 681 3 homeodomain .1 4 for pituitary development and transcription factor hormone expression A transcription factor involved in SRY (sex NG_009387 NM_005634. the regulation of embryonic SOX3 determining region 1341 1 .1 2 development and in the Y)-box 3 determination of the cell fate. A nuclear hormone receptor for Thyroid hormone NG_009159 NM_000461. triiodothyronine, mediating the THRB 1387 10 receptor, beta .1 4 biological activities of thyroid thyroid hormone hormone. resistance A nuclear hormone receptor for

Thyroid hormone NG_023345 NM_199334. triiodothyronine, mediating the Peripheral THRA 1473 9 receptor, alpha .1 3 biological activities of thyroid hypothyro hormone. idism Solute carrier family thyroid hormone 16 (monocarboxylic SLC16A2 NG_011641 NM_006517. Mediating the uptake of thyroid transprotation acid transporters), 1620 6 (MCT8) .1 4 hormones into the brain abnormality member 2 (putative transport) Functions as both a repressor and Syndromi Solute carrier family activator of transcription and is c SLC26A4( 26, member 4 NG_008489 NM_000441. specifically involved in the Pendred syndrome 2343 21 hypothyro PDS) (Pendred syndrome, .1 1 development of pancreatic beta idism PDS cells, the thyroid, eye, liver and kidney. May play an important role in the NG_012068 NM_012188. development of the cochlea and FOXI1 Forkhead box i1 1137 2 .1 4 vestibulum, as well as in embryogenesis. Functions as both a repressor and activator of transcription and is Neonatal diabetes GLIS3(ZN Glis family zinc NG_011782 NM_152629. specifically involved in the & congenital 2328 10 F515) finger 3 .1 3 development of pancreatic beta hypothyroidism cells, the thyroid, eye, liver and kidney. Thyroid Bamforth-Lazarus FOXE1 NG_011979 NM_004473. A transcription factor functions in transcription 374 1 syndrome （TTF-2） .1 3 thyroid development factor 2 A thyroid-specific transcription NKX2-1 NG_013365 :NM_001079 factor，regulates the expression of Choreoathetosis NK2 homeobox 1 402 3 (TTF-1) .1 668.2 thyroid-specific genes and genes involved in morphogenesis Ubiquitin protein Responsible for facilitating the Johanson–Blizzard NG_012182 UBR1 ligase E3 component NM_174916 1750 47 direct ubiquitination of substrate syndrome .1 n-recognin 1 A candidate gene for a patient's protein NG_12047. NM_000465. ZNF252P 5210 5 transient neonatal thyroid 252, pseudogene 2 2 Transient congenital dysfunction hypothyroidism Necessary for proper cellular Dual oxidase NG_016992 NM_207581. DUOXA2 321 6 localization and maturation of maturation factor 2 .1 3 functional dual oxidase 2. RefSeq, reference sequence; CDS, coding DNA sequence.