There are several journals focused on rare (orphan) diseases and medical genetics. Many of them provide free full-text access to all or selected articles. Below is a directory of journals with details on the open access option and impact factor (for the year 2012).
Rare (orphan) diseases journals
ξ Orphanet Journal of Rare Diseases  — open access BioMedCentral journal with impact factor 5.07. The official journal of Orpha.Net , the European portal for rare diseases and orphan drugs, that also provides a plenty of useful services and information resources (such as encyclopedia of rare disease  in several languages, reference manual of orphan drugs , list of European centers for diagnostics and treatment of rare diseases , directory of existing diagnostic tests , registry for clinical trials , directory of patient organizations  all over the world, etc).
ξ Intractable Rare Diseases Research  — open access journal with emphasis on rare diseases in Asia.
ξ Rare Diseases  — open access journal established in 2013.
ξ The Journal of Rare Disorders  — open access journal established in 2013.
ξ Journal of Inherited Metabolic Disease  — established in 1978, some articles have free full-text access.
ξ CasesDatabase  — open access collection of more than 25,000 cases from 252 journals, some of the cases represent rare diseases.
ξ Special supplement to the Journal of General Internal Medicine  dedicated to research methods for evaluating patient health outcomes in rare diseases — announced for publishing in 2014.
ξ Journal of Rare Cardiovascular Diseases  — was announced for quarterly publication, but only a table of contents for the first issue is available on the journal’s web-site, without possibility to access full-text articles.
ξ Orphan Diseases and Rare Drugs  — announced in 2013 as open access journal, currently calls for articles submission, and has no published issues.
Medical genetics journals
ξ Gene Reviews  – comprehensive open access compendium for genetic diseases (including rare diseases). Currently 592 chapters each dedicated to a separate genetic disease are available, all of them are regularly updated by leading scientists. Each chapter contains extensive information on clinical appearance, diagnostic methods, current treatment options and genetic counseling.
ξ American Journal of Human Genetics  — official journal of the American Society of Human Genetics, impact factor 10.603. All articles get an open access status within 6 months after publication.
ξ BMC Medical Genomics  — BioMedCentral-family journal with open access, impact factor 3.69.
ξ Human Genomics  — BioMedCentral-family journal with open access, impact factor 3.36.
ξ BMC Genetics  — BioMedCentral-family journal with open access, impact factor 2.48.
ξ BMC Medical Genetics  — BioMedCentral-family journal with open access, impact factor 2.33.
ξ Genome Medicine  — BioMedCentral-family journal with open access
ξ PLoS genetics  — Public Library Of Science-family journal with open access.
ξ Frontiers in Genetics  — open access journal, many articles dedicated to medical genetics.
ξ Physiological genomics  — official journal of the American Physiological Society, impact factor 2.735. All articles get open access status in 1 year after publication, some published initially as open access articles.
ξ Indian journal of human genetics  — open access journal, html version of articles is freely available for all, while pdf version could be obtained only by journal’s subscribers or visitors from India.
ξ American Journal of Medical Genetics: Part A  — impact factor 2.39, a substantial proportion of articles are in open access.
American Journal of Medical Genetics Part B: Neuropsychiatric Genetics  — impact factor 3.70, a substantial proportion of articles are in open access.
American Journal of Medical Genetics Part C: Seminars in Medical Genetics  — impact factor 4.05, a substantial proportion of articles are in open access.
ξ Annals of human genetics  — all articles put in open access 2 years after publication, while some papers published in open access immediately, impact factor 2.565.
ξ Human molecular genetics  — some articles are published under open access option, impact factor 7.636.
ξ Journal of Medical Genetics  — some articles are in open access, impact factor 6.365.
ξ Genetics in Medicine  — some articles are in open access, impact factor 4.762.
ξ Pharmacogenetics & Genomics  — some articles are in open access, impact factor 3.485.
ξ Clinical Genetics  — some articles are in open access, impact factor 3.128.
ξ Human Genetics  — few articles are in open access, impact factor 5.069.
ξ Journal of Human Genetics  — some articles are in open access, impact factor 2.496.
ξ Nature genetics  and Nature Reviews. Genetics  — are dedicated to genetics in general, there are some articles presenting issues of medical genetics (for example, the collection of articles «Disease mechanisms» ).
ξ Somatic Cell and Molecular Genetics  — some articles are in open access.
ξ Annual Review Genetics  — published annually, contains reviwes on broad spectrum of topics, available only to subscribers.
ξ European journal of medical genetics  — impact factor 2.178
ξ Forensic Science International: Genetics  — impact factor 3.08
ξ Russian Journal of Genetics  — English version of Russian journal «Genetika».