| ACTL6B | | Intellectual developmental disorder with severe speech and ambulation defects | 1~3 | 都立 | 〇 | | | | |
| ACVR1 | | Fibrodysplasia ossificans progressiva | 1~3 | 都立 | 〇 | | | | |
| ADNP | | Helsmoortel-van der Aa syndrome | 1~3 | 都立 | 〇 | | | | |
| AHDC1 | シア・ギブス症候群 | Xia-Gibbs syndrome | 1~3 | 兵庫 | 〇 | | | | |
| ANKRD11 | KBG症候群 | KBG syndrome | 1~3 | 都立 | 〇 | | | | |
| ANTXR2 | ヒアリン線維腫症候群 | Hyaline Fibromatosis Syndrome | 1~3 | 都立 | 〇 | | | | |
| ARID1B | コフィン・シリス症候群 | Coffin-Siris syndrome | 4~6 | 都立 | 〇 | | | | |
| ASXL1 | ボーリング・オピッツ症候群 | Bohring-Opitz syndrome | 1~3 | 兵庫 | 〇 | | | | |
| ATRX | ATR-X症候群 | ATRX syndrome | 1~3 | 都立 | 〇 | | | | |
| BRF1 | 小脳-顔-歯症候群 | Cerebellar-Facio-Dental syndrome | 1~3 | 都立 | 〇 | | | | |
| CASK | CASK異常症 | Intellectual developmental disorder and microcephaly with pontine and cerebellar hypoplasia | 1~3 | 都立 | 〇 | | | | |
| CBL | ヌーナン症候群 | Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia | 1~3 | 都立 | 〇 | | | | |
| CDK8 | | Intellectual developmental disorder with hypotonia and behavioral abnormalities | 1~3 | 都立 | 〇 | | | | |
| CHD3 | | Snijders Blok-Campeau syndrome | 1~3 | 兵庫 | × | | | | |
| CHD7 | チャージ症候群 | CHARGE syndrome | 1~3 | 都立 | 〇 | | | | |
| CHST3 | ラーセン症候群 | Larsen syndrome | 1~3 | 都立 | 〇 | | | | |
| CLCN6 | | Neurodegeneration, childhood-onset, hypotonia, respiratory insufficiency and brain imaging abnormalities | 1~3 | 都立 | 〇 | | | | |
| COL5A1 | 古典型エーラス・ダンロス症候群 | Ehlers-Danlos syndrome, classic type, 1 | 1~3 | 都立 | × | | | | |
| CREBBP | ルビンシュタイン・テイビ症候群 | Rubinstein-Taybi syndrome | 1~3 | 都立 | 〇 | | | | |
| CREBBP | メンケ・ヘネカム症候群 | Menke-Hennekam syndrome | 1~3 | 都立 | 〇 | | | | |
| CSNK2A1 | | Okur-Chung syndrome | 1~3 | 都立 | × | | | | |
| CTCF | | Intellectual developmental disorder, autosomal dominant 21 | 1~3 | 都立 | 〇 | | | | |
| CTNNB1 | | Neurodevelopmental disorder with spastic diplegia and visual defects | 1~3 | 都立 | 〇 | | | | |
| DCPS | Al-Raqad症候群 | Al-Raqad syndrome | 1~3 | 兵庫 | 〇 | | | | |
| DDX3X | DDX3X関連神経発達異常症 | Intellectual developmental disorder, X-linked syndromic, Snijders Blok type | 1~3 | 都立 | 〇 | | | | |
| DNMT3A | | Heyn-Sproul-Jackson syndrome | 1~3 | 都立 | 〇 | | | | |
| DVL1 | ロビノウ症候群 | Robinow syndrome | 1~3 | 都立 | 〇 | | | | |
| EFTUD2 | 下顎顔面異骨症 | Mandibulofacial dysostosis, Guion-Almeida type | 1~3 | 兵庫 | 〇 | | | | |
| EHMT1 | クリーフストラ症候群 | Kleefstra syndrome | 1~3 | 都立 | 〇 | | | | |
| EP300 | ルビンシュタイン・テイビ症候群 | Rubinstein-Taybi syndrome | 1~3 | 都立 | 〇 | | | | |
| EXOSC9 | | Pontocerebellar hypoplasia, type 1D | 1~3 | 都立 | 〇 | | | | |
| EZH2 | ウィーバー症候群 | Weaver syndrome | 1~3 | 都立 | 〇 | | | | |
| FBXO31 | | Intellectual developmental disorder, autosomal recessive 45 | 1~3 | 都立 | 〇 | | | | |
| FGFR2 | アペール症候群 | Apert syndrome | 1~3 | 都立 | 〇 | | | | |
| FGFR2 | ファイファー症候群 | Pfeiffer syndrome | 1~3 | 都立 | 〇 | | | | |
| FGFR2 | クルーゾン症候群 | Crouzon syndrome | 1~3 | 都立 | × | | | | |
| FGFR3 | 軟骨低形成症 | Hypochondroplasia | 1~3 | 都立 | 〇 | | | | |
| FGFR3 | 軟骨無形成症 | Achondroplasia | 1~3 | 都立 | 〇 | | | | |
| FLNA | 脳室周囲結節性異所性灰白質 | FLNA related periventricular heterotopia | 1~3 | 都立 | 〇 | | | | |
| FRAS1 | フレイザー症候群 | Fraser syndrome | 1~3 | 都立 | 〇 | | | | |
| HDAC8 | コルネリア・デランゲ症候群 | Cornelia de Lange syndrome | 1~3 | 都立 | 〇 | | | | |
| HECW2 | | Neurodevelopmental disorder with hypotonia, seizures, and absent language | 1~3 | 兵庫 | 〇 | | | | |
| HNRNPU | | Developmental and epileptic encephalopathy 54 | 1~3 | 都立 | 〇 | | | | |
| HRAS | コステロ症候群 | Costello syndrome | 1~3 | 都立 | 〇 | | | | |
| KAT6B | ヤング・シンプソン症候群 | Young-Simpson syndrome | 1~3 | 都立 | 〇 | | | | |
| KAT6B | Genitopatellar症候群 | Genitopatellar syndrome | 1~3 | 兵庫 | 〇 | | | | |
| KDM5C | | Intellectual developmental disorder, X-linked syndromic, Claes-Jensen type | 1~3 | 都立 | 〇 | | | | |
| KIF1A | | NESCAV syndrome | 1~3 | 都立 | 〇 | | | | |
| KMT2A | ヴィーデマン・スタイナー症候群 | Wiedemann-Steiner syndrome | 1~3 | 都立 | 〇 | | | | |
| KMT2D | 歌舞伎症候群 | Kabuki syndrome | 1~3 | 都立 | 〇 | | | | |
| LONP1 | コダス症候群 | CODAS syndrome | 1~3 | 都立 | 〇 | | | | |
| MAGEL2 | シャーフ・ヤング症候群 | Schaaf-Yang syndrome | 1~3 | 都立 | 〇 | | | | |
| MECP2 | レット症候群 | Rett syndrome | 1~3 | 都立 | 〇 | | | | |
| MEF2C | | Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language | 1~3 | 都立 | 〇 | | | | |
| MITF | ワールデンブルグ症候群 | Waardenburg syndrome, type 2A | 1~3 | 都立 | 〇 | | | | |
| MRAS | ヌーナン症候群 | Noonan syndrome | 1~3 | 都立 | 〇 | | | | |
| MTM1 | ミオチュブラーミオパチ― | Myopathy, centronuclear, X-linked | 1~3 | 都立 | 〇 | | | | |
| NFIA | | Brain malformations with or without urinary tract defects | 1~3 | 都立 | 〇 | | | | |
| NIPBL | コルネリア・デランゲ症候群 | Cornelia de Lange syndrome | 1~3 | 都立 | 〇 | | | | |
| NSD1 | ソトス症候群 | Sotos syndrome | 1~3 | 都立 | 〇 | | | | |
| NTRK1 | 先天性無痛無汗症 | Insensitivity to pain, congenital, with anhidrosis | 1~3 | 都立 | 〇 | | | | |
| PHF6 | | Borjeson-Forssman-Lehmann syndrome | 1~3 | 都立 | 〇 | | | | |
| POLR1D | トリーチャー・コリンズ症候群 | Treacher Collins syndrome | 1~3 | 都立 | 〇 | | | | |
| POMGNT2 | | Walker-Warburg syndrome | 1~3 | 都立 | 〇 | | | | |
| PPM1D | | Jansen-de Vries syndrome | 1~3 | 都立 | 〇 | | | | |
| PPP1CB | ヌーナン症候群類縁疾患 | Noonan like disorder with loose anagen hair 1 | 1~3 | 都立 | 〇 | | | | |
| PPP2R1A | | Intellectual developmental disorder, autosomal dominant 36 | 1~3 | 都立 | 〇 | | | | |
| PTEN | PTEN大頭症 | Macrocephaly/ autism syndrome | 1~3 | 都立 | 〇 | | | | |
| PTPN11 | ヌーナン症候群 | Noonan syndrome | 1~3 | 都立 | 〇 | | | | |
| RIT1 | ヌーナン症候群 | Noonan syndrome | 1~3 | 都立 | 〇 | | | | |
| RMRP | 軟骨毛髪低形成症 | Cartilage-hair hypoplasia | 1~3 | 都立 | × | | | | |
| RPS6KA3 | コフィン・ローリー症候群 | Coffin-Lowry syndrome | 1~3 | 都立 | × | | | | |
| SATB2 | グラス症候群 | Glass syndrome | 1~3 | 都立 | 〇 | | | | |
| SETD2 | | Luscan-Lumish syndrome | 1~3 | 都立 | 〇 | | | | |
| SHANK3 | フェラン・マクダーミド症候群 | Phelan-McDermid syndrome | 1~3 | 都立 | 〇 | | | | |
| SLC39A8 | 先天性グリコシル化異常症 | Congenital disorder of glycosylation, type IIn | 1~3 | 兵庫 | × | | | | |
| SLC9A6 | クリスチャンソン症候群 | Christianson syndrome | 1~3 | 都立 | 〇 | | | | |
| SMARCA2 | ニコライデス・バライスター症候群 | Nicolaides-Baraitser syndrome | 1~3 | 都立 | 〇 | | | | |
| SOX9 | 屈曲肢異形成症 | Campomelic dysplasia | 1~3 | 都立 | 〇 | | | | |
| STAG2 | | Mullegama-Klein-Martinez syndrome | 1~3 | 都立 | 〇 | | | | |
| TBCK | | Hypotonia, infantile, with psychomotor retardation and characteristic facies 3 | 1~3 | 都立 | 〇 | | | | |
| TCF4 | ピット・ホプキンス症候群 | Pitt-Hopkins syndrome | 1~3 | 兵庫 | 〇 | | | | |
| TCOF1 | トリーチャー・コリンズ症候群 | Treacher Collins syndrome | 1~3 | 都立 | 〇 | | | | |
| TRAF7 | | Cardiac, facial, and digital anomalies with developmental delay | 1~3 | 都立 | × | | | | |
| TRPV4 | 変容性骨異形成症 | Metatropic dysplasia | 1~3 | 都立 | 〇 | | | | |
| TRMT1 | | Intellectual developmental disorder, autosomal recessive 68 | 1~3 | 兵庫 | 〇 | | | | |
| TRPM3 | | Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skeletal anomalies, with or without seizures | 1~3 | 都立 | 〇 | | | | |
| TUBB2B | | Cortical dysplasia, complex, with other brain malformations 7 | 1~3 | 長野 | 〇 | | | | |
| TUBB3 | | Cortical dysplasia, complex, with other brain malformations 1 | 1~3 | 兵庫 | × | | | | |
| UBA5 | | Developmental and epileptic encephalopathy 44 | 1~3 | 都立 | 〇 | | | | |
| USP9X | | Intellectual developmental disorder, X-linked 99 | 1~3 | 都立 | 〇 | | | | |
| VPS13B | コーエン症候群 | Cohen syndrome | 1~3 | 都立 | × | | | | |
| ZC4H2 | | Wieacker-Wolff syndrome | 1~3 | 都立 | 〇 | | | | |
| ZEB2 | モワット・ウィルソン症候群 | Mowat-Wilson syndrome | 1~3 | 都立 | 〇 | | | | |
| ZSWIM6 | | Acromelic frontonasal dysostosis | 1~3 | 都立 | 〇 | | | | |