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<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" article-type="review-article" dtd-version="1.2" xml:lang="en"><front><journal-meta><journal-id journal-id-type="publisher-id">Ecological genetics</journal-id><journal-title-group><journal-title xml:lang="en">Ecological genetics</journal-title><trans-title-group xml:lang="ru"><trans-title>Экологическая генетика</trans-title></trans-title-group></journal-title-group><issn publication-format="print">1811-0932</issn><issn publication-format="electronic">2411-9202</issn><publisher><publisher-name xml:lang="en">Eco-Vector</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">695654</article-id><article-id pub-id-type="doi">10.17816/ecogen695654</article-id><article-id pub-id-type="edn">GWZOCX</article-id><article-categories><subj-group subj-group-type="toc-heading" xml:lang="en"><subject>Human ecological genetics</subject></subj-group><subj-group subj-group-type="toc-heading" xml:lang="ru"><subject>Экологическая генетика человека</subject></subj-group><subj-group subj-group-type="article-type"><subject>Review Article</subject></subj-group></article-categories><title-group><article-title xml:lang="en">Cystinuria in clinical practice: challenges in genetic verification and laboratory diagnosis</article-title><trans-title-group xml:lang="ru"><trans-title>Цистинурия в клинической практике: сложности генетической верификации и клинико-лабораторной диагностики</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0005-1124-3360</contrib-id><contrib-id contrib-id-type="spin">1019-8610</contrib-id><name-alternatives><name xml:lang="en"><surname>Luganskaya</surname><given-names>Polina S.</given-names></name><name xml:lang="ru"><surname>Луганская</surname><given-names>Полина Сергеевна</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Center for Transgenesis and Genome Editing</p></bio><bio xml:lang="ru"><p>Центр трансгенеза и редактирования генома</p></bio><email>polina.luganskaja@yandex.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0007-4108-6161</contrib-id><contrib-id contrib-id-type="spin">7921-4448</contrib-id><name-alternatives><name xml:lang="en"><surname>Kandina</surname><given-names>Daria A.</given-names></name><name xml:lang="ru"><surname>Кандина</surname><given-names>Дарья Алексеевна</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Center for Transgenesis and Genome Editing</p></bio><bio xml:lang="ru"><p>Центр трансгенеза и редактирования генома</p></bio><email>candyda20@mail.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0008-8920-6705</contrib-id><contrib-id contrib-id-type="spin">5952-4539</contrib-id><name-alternatives><name xml:lang="en"><surname>Akhmarov</surname><given-names>Ilyas I.</given-names></name><name xml:lang="ru"><surname>Ахмаров</surname><given-names>Ильяс Идрисович</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Center for Transgenesis and Genome Editing</p></bio><bio xml:lang="ru"><p>Центр трансгенеза и редактирования генома</p></bio><email>luvk7411@yandex.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0004-3400-6678</contrib-id><contrib-id contrib-id-type="spin">7459-9945</contrib-id><name-alternatives><name xml:lang="en"><surname>Kirillov</surname><given-names>Oleg A.</given-names></name><name xml:lang="ru"><surname>Кириллов</surname><given-names>Олег Андреевич</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Center for Transgenesis and Genome Editing</p></bio><bio xml:lang="ru"><p>Центр трансгенеза и редактирования генома</p></bio><email>o-kirillov03@mail.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-7825-273X</contrib-id><contrib-id contrib-id-type="spin">6019-1547</contrib-id><name-alternatives><name xml:lang="en"><surname>Sopova</surname><given-names>Julia V.</given-names></name><name xml:lang="ru"><surname>Сопова</surname><given-names>Юлия Викторовна</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Cand. Sci. (Biology), Center for Transgenesis and Genome Editing</p></bio><bio xml:lang="ru"><p>канд. биол. наук, Центр трансгенеза и редактирования генома</p></bio><email>sopova@hotmail.com</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-0236-3302</contrib-id><contrib-id contrib-id-type="spin">2573-1759</contrib-id><name-alternatives><name xml:lang="en"><surname>Leonova</surname><given-names>Elena I.</given-names></name><name xml:lang="ru"><surname>Леонова</surname><given-names>Елена Ивановна</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Cand. Sci. (Biology), Center for Transgenesis and Genome Editing</p></bio><bio xml:lang="ru"><p>канд. биол. наук, Центр трансгенеза и редактирования генома</p></bio><email>1102.elena@gmail.com</email><xref ref-type="aff" rid="aff1"/></contrib></contrib-group><aff-alternatives id="aff1"><aff><institution xml:lang="en">Saint Petersburg State University</institution></aff><aff><institution xml:lang="ru">Санкт-Петербургский государственный университет</institution></aff></aff-alternatives><pub-date date-type="preprint" iso-8601-date="2026-04-01" publication-format="electronic"><day>01</day><month>04</month><year>2026</year></pub-date><pub-date date-type="pub" iso-8601-date="2026-07-02" publication-format="electronic"><day>02</day><month>07</month><year>2026</year></pub-date><volume>24</volume><issue>2</issue><issue-title xml:lang="en"/><issue-title xml:lang="ru"/><fpage>159</fpage><lpage>165</lpage><history><date date-type="received" iso-8601-date="2025-10-31"><day>31</day><month>10</month><year>2025</year></date><date date-type="accepted" iso-8601-date="2026-03-29"><day>29</day><month>03</month><year>2026</year></date></history><permissions><copyright-statement xml:lang="en">Copyright ©; 2026, Eco-Vector</copyright-statement><copyright-statement xml:lang="ru">Copyright ©; 2026, Эко-Вектор</copyright-statement><copyright-year>2026</copyright-year><copyright-holder xml:lang="en">Eco-Vector</copyright-holder><copyright-holder xml:lang="ru">Эко-Вектор</copyright-holder><license><ali:license_ref xmlns:ali="http://www.niso.org/schemas/ali/1.0/">https://eco-vector.com/for_authors.php#07</ali:license_ref></license></permissions><self-uri xlink:href="https://journals.eco-vector.com/ecolgenet/article/view/695654">https://journals.eco-vector.com/ecolgenet/article/view/695654</self-uri><abstract xml:lang="en"><p>Cystinuria is an inherited disorder caused by impaired reabsorption of cystine and dibasic amino acids—ornithine, lysine, and arginine—in the proximal renal tubules. Ornithine, arginine, and lysine are highly soluble in urine, but the solubility of cystine depends on pH and is low under physiological conditions. The genetic basis of cystinuria involves mutations in the SLC3A1 gene (encoding the heavy subunit rBAT of the Na<sup>+</sup>-independent amino acid transporter (rBAT-b<sup>0,+</sup>AT) and the SLC7A9 gene (encoding the light subunit b<sup>0,+</sup>AT). Dysfunction of the rBAT-b<sup>0,+</sup>AT transporter leads to excessive cystine excretion, promoting urine supersaturation, crystallization, and the formation of cystine stones. Mutations in SLC7A9 exhibit a broad inheritance spectrum, ranging from recessive to dominant. Mutations in SLC3A1 are usually considered autosomal recessive; heterozygous carriers of these mutations mostly have a normal urinary amino acid profile, whereas homozygotes exhibit various symptoms of cystinuria. Accumulating clinical evidence reveals genotypic–phenotypic discordance that challenges this classical model. This review systematizes atypical cases where heterozygous carriers of pathogenic SLC3A1 mutations manifest recurrent cystine stones and hypercystinuria, whereas family members with identical mutations remain asymptomatic. Notably, approximately 10% of patients lack detectable mutations in the coding regions of these genes, suggesting the potential involvement of non-coding regulatory regions or modifier genes, including but not limited to SLC7A10 (ASC1), SLC1A5 (ASCT2), and SLC7A13 (AGT1). The review concludes that additional methods, such as whole-genome sequencing of well-characterized families, are necessary to identify these hidden genetic factors, improve diagnostic accuracy, and better understand the molecular mechanisms underlying cystinuria.</p></abstract><trans-abstract xml:lang="ru"><p>Цистинурия — это наследственное заболевание, обусловленное нарушением реабсорбции цистина и двухосновных аминокислот — орнитина, лизина и аргинина — в проксимальных канальцах почек. К развитию цистинурии приводят мутации в гене SLC3A1 (кодирует тяжёлую субъединицу rBAT натрий-независимого переносчика аминокислот rBAT-b⁰<sup>,+</sup>AT) и в гене SLC7A9 (кодирует лёгкую субъединицу b⁰<sup>,+</sup>AT). Орнитин, аргинин и лизин хорошо растворимы в моче, тогда как растворимость цистина зависит от pH и при физиологических значениях является низкой. Дисфункция переносчика rBAT-b⁰<sup>,+</sup>AT приводит к избыточной экскреции цистина, способствуя перенасыщению мочи, кристаллизации цистина и образованию цистиновых камней. Мутации в гене SLC7A9 демонстрируют как рецессивный, так и доминантный типы наследования. Мутации в гене SLC3A1 обычно рассматриваются как аутосомно-рецессивные, и гетерозиготные носители этих мутаций в большинстве случаев имеют нормальный аминокислотный профиль мочи, тогда как у гомозиготных пациентов проявляются различные симптомы цистинурии. Накопление клинических данных в сочетании с данными генетических исследований пациентов выявляет генотип-фенотипические несоответствия, которые противоречат этой классической модели. Данный обзор систематизирует атипичные случаи, в которых у гетерозиготных носителей патогенных генетических вариантов в гене SLC3A1 наблюдаются рецидивирующие цистиновые камни и гиперцистинурия, тогда как члены их семей с идентичными мутациями остаются бессимптомными. Примечательно, что примерно у 10% пациентов с цистинурией не обнаруживается каких-либо патогенных генетических вариантов в кодирующих областях генов SLC3A1 и SLC7A9, что предполагает потенциальное наличие нарушений в некодирующих регуляторных регионах или в генах-модификаторах, в число которых могут входить SLC7A10 (ASC1), SLC1A5 (ASCT2) и SLC7A13 (AGT1). В обзоре сделан вывод, что для выявления этих скрытых генетических факторов, улучшения диагностики и более глубокого понимания молекулярных механизмов цистинурии необходимо применение дополнительных методов исследования, таких как полногеномное секвенирование пациентов и их родственников.</p></trans-abstract><kwd-group xml:lang="en"><kwd>SLC3A1</kwd><kwd>SLC7A9</kwd><kwd>cystinuria</kwd><kwd>amino acid transporter</kwd><kwd>inherited kidney diseases</kwd></kwd-group><kwd-group xml:lang="ru"><kwd>SLC3A1</kwd><kwd>SLC7A9</kwd><kwd>цистинурия</kwd><kwd>транспортер аминокислот</kwd><kwd>наследственные заболевания почек</kwd></kwd-group><funding-group><award-group><funding-source><institution-wrap><institution xml:lang="en">Saint Petersburg State University</institution></institution-wrap><institution-wrap><institution xml:lang="ru">Санкт-Петербургский государственный университет</institution></institution-wrap></funding-source><award-id>148726920</award-id></award-group><funding-statement xml:lang="en">This work was supported by St. Petersburg State University, Project ID 148726920</funding-statement><funding-statement xml:lang="ru">Исследование выполнено при финансовой поддержке гранта СПбГУ PURE ID 148726920</funding-statement></funding-group></article-meta></front><body></body><back><ref-list><ref id="B1"><label>1.</label><mixed-citation>Scriver CR. 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