- Short stature (HP:0004322): A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms). Evidence: IEA. (OMIM:309583)
- Seizure (HP:0001250): A seizure is an intermittent abnormality of nervous system physiology characterized by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. Evidence: IEA. (OMIM:309583)
- Decreased muscle mass (HP:0003199). Evidence: IEA. (OMIM:309583)
- Hypotonia (HP:0001252): Hypotonia is an abnormally low muscle tone (the amount of tension or resistance to movement in a muscle). Even when relaxed, muscles have a continuous and passive partial contraction which provides some resistance to passive stretching. Hypotonia thus manifests as diminished resistance to passive stretching. Hypotonia is not the same as muscle weakness, although the two conditions can co-exist. Evidence: IEA. (OMIM:309583)
- Generalized hypotonia (HP:0001290): Generalized muscular hypotonia (abnormally low muscle tone). Evidence: TAS. (OMIM:309583)
- Narrow palm (HP:0004283): For children from birth to 4 years of age, the palm width is more than 2 SD below the mean; for children from 4 to 16 years of age the palm width is below the 5th centile; or, the width of the palm appears disproportionately narrow for its length. Evidence: TAS. (OMIM:309583)
- Sparse eyebrow (HP:0045075): Decreased density/number of eyebrow hairs. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Smooth philtrum (HP:0000319): Flat skin surface, with no ridge formation in the central region of the upper lip between the nasal base and upper vermilion border. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Hoarse voice (HP:0001609): Hoarseness refers to a change in the pitch or quality of the voice, with the voice sounding weak, very breathy, scratchy, or husky. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Hypertelorism (HP:0000316): Interpupillary distance more than 2 SD above the mean (alternatively, the appearance of an increased interpupillary distance or widely spaced eyes). Evidence: IEA. (OMIM:309583)
- Single transverse palmar crease (HP:0000954): The distal and proximal transverse palmar creases are merged into a single transverse palmar crease. Evidence: PCS. Frequency: 1/2. (PMID:19206178)
- Long fingers (HP:0100807): The middle finger is more than 2 SD above the mean for newborns 27 to 41 weeks EGA or above the 97th centile for children from birth to 16 years of age AND the five digits retain their normal length proportions relative to each other (i.e., it is not the case that the middle finger is the only lengthened digit), or, Fingers that appear disproportionately long compared to the palm of the hand. Evidence: TAS. (OMIM:309583)
- Dental crowding (HP:0000678): Changes in alignment of teeth in the dental arch. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Long hallux (HP:0001847): Increased length of the big toe. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Intellectual disability (HP:0001249): The term intellectual disability or intellectual developmental disorder is used to describe significantly sub-average intellectual and adaptive functioning based on clinical assessment and as measured by individually administered, appropriately normed, standardized and validated tests of intellectual functioning and adaptive behavior, with onset during the developmental period from infancy through adolescence. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Kyphoscoliosis (HP:0002751): An abnormal curvature of the spine in both a coronal (lateral) and sagittal (back-to-front) plane. Evidence: PCS. Frequency: 1/2. (PMID:19206178)
- Cleft palate (HP:0000175): Cleft palate is a developmental defect of the palate resulting from a failure of fusion of the palatine processes and manifesting as a separation of the roof of the mouth (soft and hard palate). Evidence: IEA. (OMIM:309583)
- Hyperextensibility of the finger joints (HP:0001187): The ability of the finger joints to move beyond their normal range of motion. Evidence: TAS. (OMIM:309583)
- Tall stature (HP:0000098): A height above that which is expected according to age and gender norms. Evidence: IEA. (OMIM:309583)
- Dysarthria (HP:0001260): Dysarthric speech is a general description referring to a neurological speech disorder characterized by poor articulation. Depending on the involved neurological structures, dysarthria may be further classified as spastic, flaccid, ataxic, hyperkinetic and hypokinetic, or mixed. Evidence: IEA. (OMIM:309583)
- Global developmental delay (HP:0001263): A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- High myopia (HP:0011003): A severe form of myopia with greater than -6.00 diopters. Evidence: IEA. (OMIM:309583)
- X-linked recessive inheritance (HP:0001419): A mode of inheritance that is observed for recessive traits related to a gene encoded on the X chromosome. In the context of medical genetics, X-linked recessive disorders manifest in males (who have one copy of the X chromosome and are thus hemizygotes), but generally not in female heterozygotes who have one mutant and one normal allele. Evidence: PCS. (PMID:19206178)
- Pectus excavatum (HP:0000767): A defect of the chest wall characterized by a depression of the sternum, giving the chest ("pectus") a caved-in ("excavatum") appearance. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- High, narrow palate (HP:0002705): The presence of a high and narrow palate. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Pectus carinatum (HP:0000768): A deformity of the chest caused by overgrowth of the ribs and characterized by protrusion of the sternum. Evidence: IEA. (OMIM:309583)
- Short philtrum (HP:0000322): Distance between nasal base and midline upper lip vermilion border more than 2 SD below the mean. Alternatively, an apparently decreased distance between nasal base and midline upper lip vermilion border. Evidence: IEA. (OMIM:309583)
- Brachycephaly (HP:0000248): An abnormality of skull shape characterized by a decreased anterior-posterior diameter. That is, a cephalic index greater than 81%. Alternatively, an apparently shortened anteroposterior dimension (length) of the head compared to width. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Facial asymmetry (HP:0000324): An abnormal difference between the left and right sides of the face. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Hypernasal speech (HP:0001611): A type of speech characterized by the presence of an abnormally increased nasal airflow during speech associated with structural abnormality of the nasal passages. Evidence: PCS. (PMID:19206178)
- Anteverted nares (HP:0000463): Anteriorly-facing nostrils viewed with the head in the Frankfurt horizontal and the eyes of the observer level with the eyes of the subject. This gives the appearance of an upturned nose (upturned nasal tip). Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Thickened calvaria (HP:0002684): The presence of an abnormally thick calvaria. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Osteoporosis (HP:0000939): Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO criteria, osteoporosis is defined as a BMD that lies 2.5 standard deviations or more below the average value for young healthy adults (a T-score below -2.5 SD). Evidence: IEA. (OMIM:309583)
- Bulbous nose (HP:0000414): Increased volume and globular shape of the anteroinferior aspect of the nose. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Recurrent fractures (HP:0002757): The repeated occurrence of bone fractures (implying an abnormally increased tendency for fracture). Evidence: PCS. Frequency: 1/2. (PMID:19206178)
- Wide intermamillary distance (HP:0006610): A larger than usual distance between the left and right nipple. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Vertebral compression fracture (HP:0002953). Evidence: PCS. Frequency: 1/2. (PMID:19206178)
- Abnormal pinna morphology (HP:0000377): An abnormality of the pinna, which is also referred to as the auricle or external ear. Evidence: IEA. (OMIM:309583)
- Thick lower lip vermilion (HP:0000179): Increased thickness of the lower lip, leading to a prominent appearance of the lower lip. The height of the vermilion of the lower lip in the midline is more than 2 SD above the mean. Alternatively, an apparently increased height of the vermilion of the lower lip in the frontal view (subjective). Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Thin bony cortex (HP:0002753): Abnormal thinning of the cortical region of bones. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Broad-based gait (HP:0002136): An abnormal gait pattern in which persons stand and walk with their feet spaced widely apart. This is often a component of cerebellar ataxia. Evidence: IEA. (OMIM:309583)
- Talipes equinovarus (HP:0001762): Talipes equinovarus (also called clubfoot) typically has four main components: inversion and adduction of the forefoot; inversion of the heel and hindfoot; equinus (limitation of extension) of the ankle and subtalar joint; and internal rotation of the leg. Evidence: IEA. (OMIM:309583)
- Scoliosis (HP:0002650): The presence of an abnormal lateral curvature of the spine. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Bifid uvula (HP:0000193): Uvula separated into two parts most easily seen at the tip. Evidence: IEA. (OMIM:309583)
- Short neck (HP:0000470): Diminished length of the neck. Evidence: PCS. Frequency: 1/2. (PMID:19206178)
- Long palm (HP:0011302): For children from birth to 16 years of age the length of the palm is more than the 97th centile; or, the length of the palm appears relatively long compared to the finger length or the limb length. Evidence: TAS. (OMIM:309583)
- Ptosis (HP:0000508): The upper eyelid margin is positioned 3 mm or more lower than usual and covers the superior portion of the iris (objective); or, the upper lid margin obscures at least part of the pupil (subjective). Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Prominent nasal bridge (HP:0000426): Anterior positioning of the nasal root in comparison to the usual positioning for age. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Synophrys (HP:0000664): Meeting of the medial eyebrows in the midline. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Webbed neck (HP:0000465): Pterygium colli is a congenital skin fold that runs along the sides of the neck down to the shoulders. It involves an ectopic fibrotic facial band superficial to the trapezius muscle. Excess hair-bearing skin is also present and extends down the cervical region well beyond the normal hairline. Evidence: PCS. Frequency: 2/2. (PMID:19206178)
- Cryptorchidism (HP:0000028): Testis in inguinal canal. That is, absence of one or both testes from the scrotum owing to failure of the testis or testes to descend through the inguinal canal to the scrotum. Evidence: IEA. (OMIM:309583)
- Mandibular prognathia (HP:0000303): Abnormal prominence of the chin related to increased length of the mandible. Evidence: IEA. (OMIM:309583)
These phenotypes are associated with the disease syndromic X-linked intellectual disability Snyder type (OMIM:309583).