syndromic X-linked intellectual disability Siderius type

Summary

syndromic X-linked intellectual disability Siderius type (MONDO:0010286) is a disease caused by PHF8 (GenCC Definitive), with 1 cohort gene.

At a glance

• Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
• Causal gene: PHF8 (GenCC Definitive)
• Cohort genes: 1
• ClinVar variants: 45
• Phenotypes (HPO): 12

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Cases/families		2	Worldwide	Validated
Point prevalence	<1 / 1 000 000		Worldwide	Validated

Signs & symptoms

Clinical features (HPO)

12 HPO clinical features (Orphanet curated; top 12 by frequency):

HPO ID	Term	Frequency
HP:0000202	Orofacial cleft	Very frequent (80-99%)
HP:0000204	Cleft upper lip	Very frequent (80-99%)
HP:0000276	Long face	Very frequent (80-99%)
HP:0000455	Broad nasal tip	Very frequent (80-99%)
HP:0001176	Large hands	Very frequent (80-99%)
HP:0001256	Intellectual disability, mild	Very frequent (80-99%)
HP:0000028	Cryptorchidism	Frequent (30-79%)
HP:0008734	Decreased testicular size	Frequent (30-79%)
HP:0000664	Synophrys	Occasional (5-29%)
HP:0001177	Preaxial hand polydactyly	Occasional (5-29%)
HP:0002162	Low posterior hairline	Occasional (5-29%)
HP:0002650	Scoliosis	Occasional (5-29%)

Identifiers

Disease identifiers

Field	Value
Canonical name	syndromic X-linked intellectual disability Siderius type
Mondo ID	MONDO:0010286
MeSH	C537333
OMIM	300263
Orphanet	85287
DOID	DOID:0060812
UMLS	C1846055
MedGen	337375
GARD	0009704
Is cancer (heuristic)	no

Also known as: intellectual deficit X-linked Siderius type · intellectual developmental disorder, X-linked, syndromic, Siderius type, X-linked recessive · intellectual disability syndrome, X-linked, Siderius type · intellectual disability X-linked Siderius type · mental retardation X-linked Siderius type · mental retardation, X-linked, syndromic, Siderius type · MRXSSD · Siderius Hamel syndrome · Siderius X-linked intellectual disability syndrome · Siderius X-linked mental retardation syndrome · Siderius-Hamel syndrome · syndromic X-linked intellectual disability Siderius type · X-linked intellectual disability Hamel type · X-linked mental retardation Hamel type

Data availability: 45 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › congenital nervous system disorder › syndromic X-linked intellectual disability Siderius type

Related subtypes (216): polymicrogyria, congenital myasthenic syndrome with tubular aggregates, prenatal-onset spinal muscular atrophy with congenital bone fractures, anencephaly, cerebral cavernous malformation, meningocele, progressive external ophthalmoplegia, congenital nystagmus, congenital toxoplasmosis, congenital contractural arachnodactyly, congenital trigeminal anesthesia, familial congenital palsy of trochlear nerve, Myhre syndrome, Aase-Smith syndrome, KBG syndrome, autosomal dominant primary microcephaly, Mobius syndrome, MYH7-related skeletal myopathy, congenital stationary night blindness autosomal dominant 2, Prader-Willi syndrome, congenital myopathy 7A, myosin storage, autosomal dominant, Smith-Magenis syndrome, spina bifida, Freeman-Sheldon syndrome, isolated cerebellar hypoplasia/agenesis, Chediak-Higashi syndrome, Cohen syndrome, multiple pterygium-malignant hyperthermia syndrome, corpus callosum, agenesis of, congenital lactic acidosis, Saguenay-Lac-Saint-Jean type, facial dysmorphism-macrocephaly-myopia-Dandy-Walker malformation syndrome, diastematomyelia, EEM syndrome, Mowat-Wilson syndrome, Johanson-Blizzard syndrome, intellectual disability, Buenos-Aires type, myasthenia, congenital, refractory to acetylcholinesterase inhibitors, congenital myasthenic syndrome 6, Bailey-Bloch congenital myopathy, congenital stationary night blindness 1B, radioulnar synostosis-developmental delay-hypotonia syndrome, Schinzel-Giedion syndrome, schizencephaly, intellectual disability, Wolff type, X-linked intellectual disability-plagiocephaly syndrome, X-linked adrenal hypoplasia congenita, syndromic X-linked intellectual disability 7, syndromic X-linked intellectual disability Shashi type, syndromic X-linked intellectual disability Lubs type, syndromic X-linked intellectual disability Abidi type, X-linked intellectual disability, Cabezas type, X-linked intellectual disability-cubitus valgus-dysmorphism syndrome, syndromic X-linked intellectual disability Claes-Jensen type, moyamoya angiopathy-short stature-facial dysmorphism-hypergonadotropic hypogonadism syndrome, multiple congenital anomalies-hypotonia-seizures syndrome 2, developmental and epileptic encephalopathy, 36, blepharophimosis - intellectual disability syndrome, MKB type, X-linked intellectual disability-short stature-overweight syndrome, intellectual disability, X-linked, syndromic 33, syndromic X-linked intellectual disability 34, infantile-onset X-linked spinal muscular atrophy, syndromic X-linked intellectual disability 5, holoprosencephaly-hypokinesia-congenital contractures syndrome, X-linked intellectual disability with marfanoid habitus, Wieacker-Wolff syndrome, MERRF syndrome, macrocephaly-spastic paraplegia-dysmorphism syndrome, intellectual disability-sparse hair-brachydactyly syndrome, myofibrillar myopathy 1, isolated hereditary congenital facial paralysis, fibrosis of extraocular muscles, congenital, 2, Pierpont syndrome, congenital cataracts-facial dysmorphism-neuropathy syndrome, Bohring-Opitz syndrome, PHACE syndrome, B4GALT1-congenital disorder of glycosylation, developmental malformations-deafness-dystonia syndrome, sensory ataxic neuropathy, dysarthria, and ophthalmoparesis, AICA-ribosiduria, myofibrillar myopathy 3, fibrosis of extraocular muscles, congenital, 3c, myofibrillar myopathy 4, myofibrillar myopathy 5, cone-rod synaptic disorder, congenital nonprogressive, congenital stationary night blindness autosomal dominant 3, congenital stationary night blindness autosomal dominant 1, intellectual disability, autosomal recessive 12, progressive myoclonic epilepsy type 3, chromosome 15q13.3 microdeletion syndrome, combined pituitary hormone deficiencies, genetic form, congenital stationary night blindness 1D, DYRK1A-related intellectual disability syndrome, Pitt-Hopkins-like syndrome 2, developmental and epileptic encephalopathy, 15, Schuurs-Hoeijmakers syndrome, severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome, severe intellectual disability-progressive spastic diplegia syndrome, hypotonia, infantile, with psychomotor retardation and characteristic facies, developmental and epileptic encephalopathy, 18, CTCF-related neurodevelopmental disorder, autism spectrum disorder due to AUTS2 deficiency, developmental and epileptic encephalopathy, 23, ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder, Bardet-Biedl syndrome 11, cerebellar-facial-dental syndrome, fibrosis of extraocular muscles, congenital, 5, congenital myasthenic syndrome 15, lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome, autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome, congenital myasthenic syndrome 18, autosomal recessive spinocerebellar ataxia 20, Houge-Janssens syndrome 1, intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome, congenital stationary night blindness 1G, hypomyelinating leukodystrophy 10, developmental and epileptic encephalopathy, 50, congenital insensitivity to pain-hypohidrosis syndrome, macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome, SLC39A8-CDG, spastic paraplegia-severe developmental delay-epilepsy syndrome, cardiac anomalies - developmental delay - facial dysmorphism syndrome, severe intellectual disability-corpus callosum agenesis-facial dysmorphism-cerebellar ataxia syndrome, intellectual disability, autosomal recessive 53, TELO2-related intellectual disability-neurodevelopmental disorder, micrognathia-recurrent infections-behavioral abnormalities-mild intellectual disability syndrome, autosomal recessive limb-girdle muscular dystrophy type 2Y, myofibrillar myopathy 7, short stature-brachydactyly-obesity-global developmental delay syndrome, autosomal recessive limb-girdle muscular dystrophy type 2R1, severe microbrachycephaly-intellectual disability-athetoid cerebral palsy syndrome, congenital laryngeal palsy, congenital or early infantile CACH syndrome, congenital epulis, severe congenital nemaline myopathy, intermediate nemaline myopathy, typical nemaline myopathy, childhood-onset nemaline myopathy, adult-onset nemaline myopathy, qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan, holoprosencephaly, congenital insensitivity to pain with hyperhidrosis, congenital hydrocephalus, familial congenital mirror movements, macrocephaly-short stature-paraplegia syndrome, cephalocele, mitochondrial neurogastrointestinal encephalomyopathy, X-linked intellectual disability-hypogonadism-ichthyosis-obesity-short stature syndrome, 7p22.1 microduplication syndrome, congenital achiasma, congenital retinal arteriovenous communication, 3q27.3 microdeletion syndrome, Prader-Willi-like syndrome, 9q31.1q31.3 microdeletion syndrome, congenital oculomotor nerve palsy, congenital abducens nerve palsy, neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome, congenital insensitivity to pain with severe intellectual disability, X-linked intellectual disability-cerebellar hypoplasia-spondylo-epiphyseal dysplasia syndrome, global developmental delay-visual anomalies-progressive cerebellar atrophy-truncal hypotonia syndrome, lissencephaly spectrum disorders, hyaline body myopathy, 22q11.2 deletion syndrome, craniorachischisis, Leber congenital amaurosis, Ritscher-Schinzel syndrome, Rubinstein-Taybi syndrome, X-linked intellectual disability-hypogammaglobulinemia-progressive neurological deterioration syndrome, X-linked intellectual disability-epilepsy-progressive joint contractures-dysmorphism syndrome, X-linked intellectual disability, Pai type, X-linked intellectual disability, Stevenson type, X-linked intellectual disability, Stoll type, congenital muscular dystrophy, congenital vitreoretinal dysplasia, periventricular nodular heterotopia, postsynaptic congenital myasthenic syndrome, subcortical band heterotopia, congenital fibrosis of extraocular muscles type 1, Al Gazali Khidr Prem Chandran syndrome, distal arthrogryposis Moore weaver type, congenital myotonic dystrophy, myasthenic syndrome, congenital, 7B, presynaptic, autosomal recessive, intellectual disability, autosomal dominant 47, intellectual disability, autosomal dominant 48, spondyloepiphyseal dysplasia, sensorineural hearing loss, impaired intellectual development, and leber congenital amaurosis, myasthenic syndrome, congenital, 23, presynaptic, myasthenic syndrome, congenital, 24, presynaptic, myasthenic syndrome, congenital, 25, presynaptic, developmental and epileptic encephalopathy, 77, night blindness, congenital stationary, type1i, neuropathy, congenital hypomelinating, congenital axonal neuropathy with encephalopathy, developmental and epileptic encephalopathy, 73, PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome, isolated exencephaly, myasthenic syndrome, congenital, 22, intellectual developmental disorder with gastrointestinal difficulties and high pain threshold, intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies, 9q33.3q34.11 microdeletion syndrome, congenital labioscrotal agenesis-cerebellar malformation-corneal dystrophy-facial dysmorphism syndrome, early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome, SIN3A-related intellectual disability syndrome, childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder, X-linked congenital stationary night blindness, neurodevelopmental disorder with progressive microcephaly, spasticity, and brain anomalies, FOXG1 disorder, alpha-actinopathy, TPM3-related myopathy, X-linked recessive mitochondrial myopathy, RYR1-related myopathy, TTN-related myopathy, TPM2-related myopathy, myopathy caused by variation in POMGNT1, central hypoventilation syndrome, congenital, 1, with or without Hirschsprung disease, segmental spinal dysgenesis, myopathy, myofibrillar, 13, with rimmed vacuoles, congenital neuronal ceroid lipofuscinosis 10

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

45 retrieved; paginated sample, class counts are floors:

22 uncertain significance, 8 likely pathogenic, 7 pathogenic, 4 conflicting classifications of pathogenicity, 1 benign, 1 pathogenic/likely pathogenic, 1 benign/likely benign, 1 not provided

ClinVar	Variant (HGVS)	Gene	Classification	Review
10797	NM_015107.3(PHF8):c.943_946+8del	PHF8	Pathogenic	no assertion criteria provided
10798	NM_015107.3(PHF8):c.631C>T (p.Arg211Ter)	PHF8	Pathogenic	no assertion criteria provided
10799	NM_015107.3(PHF8):c.529A>T (p.Lys177Ter)	PHF8	Pathogenic	no assertion criteria provided
10800	NM_015107.3(PHF8):c.836T>C (p.Phe279Ser)	PHF8	Pathogenic	no assertion criteria provided
1878824	NM_015107.3(PHF8):c.2257C>T (p.Arg753Ter)	PHF8	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2572004	NM_015107.3(PHF8):c.738dup (p.His247fs)	PHF8	Pathogenic	no assertion criteria provided
374402	NM_015107.3(PHF8):c.377del (p.Leu126fs)	PHF8	Pathogenic	no assertion criteria provided
984633	NM_015107.3(PHF8):c.1880del (p.Lys627fs)	PHF8	Pathogenic	no assertion criteria provided
2431835	NM_015107.3(PHF8):c.1995+1G>A	PHF8	Likely pathogenic	criteria provided, single submitter
3065563	NM_015107.3(PHF8):c.2656C>T (p.Gln886Ter)	PHF8	Likely pathogenic	criteria provided, single submitter
3382447	NM_015107.3(PHF8):c.1516C>T (p.Arg506Ter)	PHF8	Likely pathogenic	criteria provided, single submitter
3598414	NM_015107.3(PHF8):c.1324-2A>C	PHF8	Likely pathogenic	criteria provided, single submitter
3776255	NM_015107.3(PHF8):c.2129+1G>C	PHF8	Likely pathogenic	criteria provided, single submitter
4280332	NM_015107.3(PHF8):c.718C>T (p.Arg240Ter)	PHF8	Likely pathogenic	criteria provided, single submitter
666346	NM_015107.3(PHF8):c.2444-2A>G	PHF8	Likely pathogenic	criteria provided, single submitter
930732	NM_015107.3(PHF8):c.2455del (p.Leu819fs)	PHF8	Likely pathogenic	criteria provided, single submitter
1324891	NM_015107.3(PHF8):c.1731-2A>G	PHF8	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
194540	NM_015107.3(PHF8):c.1731-1G>A	PHF8	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
2434687	NM_015107.3(PHF8):c.2132A>C (p.Glu711Ala)	PHF8	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
3358940	NM_015107.3(PHF8):c.1731-1G>C	PHF8	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1030277	NM_015107.3(PHF8):c.-56C>T	PHF8	Uncertain significance	criteria provided, single submitter
1030278	NM_015107.3(PHF8):c.2129+39G>C	PHF8	Uncertain significance	criteria provided, single submitter
1030412	NM_015107.3(PHF8):c.1185T>C (p.His395=)	PHF8	Uncertain significance	criteria provided, single submitter
1030413	NM_015107.3(PHF8):c.1349A>G (p.Lys450Arg)	PHF8	Uncertain significance	criteria provided, single submitter
1030461	NM_015107.3(PHF8):c.197G>A (p.Arg66His)	PHF8	Uncertain significance	criteria provided, multiple submitters, no conflicts
1030462	NM_015107.3(PHF8):c.2345G>C (p.Arg782Pro)	PHF8	Uncertain significance	criteria provided, single submitter
1303569	NM_015107.3(PHF8):c.2117A>G (p.Tyr706Cys)	PHF8	Uncertain significance	criteria provided, multiple submitters, no conflicts
1699452	NM_015107.3(PHF8):c.2492G>A (p.Arg831Gln)	PHF8	Uncertain significance	criteria provided, single submitter
1802561	NM_015107.3(PHF8):c.865A>T (p.Asn289Tyr)	PHF8	Uncertain significance	criteria provided, single submitter
1804980	NM_015107.3(PHF8):c.2318G>C (p.Arg773Pro)	PHF8	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 4 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
PHF8	Definitive	X-linked	syndromic X-linked intellectual disability Siderius type	4

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
PHF8	Orphanet:85287	X-linked intellectual disability, Siderius type

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
PHF8	HGNC:20672	ENSG00000172943	Q9UPP1	Histone lysine demethylase PHF8	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
PHF8	Histone lysine demethylase PHF8	Histone lysine demethylase with selectivity for mono- and dimethylated residues.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 0 · Druggable fraction: 0.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Transcription factor	1	8.3×	0.121

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
PHF8	Transcription factor	no	1.14.11.65	Znf_PHD, JmjC_dom, Znf_FYVE_PHD

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
left testis	1
right testis	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
PHF8	251	ubiquitous	marker	right testis, sural nerve, left testis

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
PHF8	2,579

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
PHF8	Q9UPP1	6

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 2. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
HDMs demethylate histones	1	228.4×	0.006	PHF8
Condensation of Prophase Chromosomes	1	156.4×	0.006	PHF8

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
negative regulation of rDNA heterochromatin formation	1	8426.0×	9e-04	PHF8
positive regulation of transcription by RNA polymerase I	1	648.1×	0.006	PHF8
G1/S transition of mitotic cell cycle	1	200.6×	0.013	PHF8
brain development	1	79.5×	0.022	PHF8
chromatin remodeling	1	73.0×	0.022	PHF8
positive regulation of DNA-templated transcription	1	27.9×	0.048	PHF8
positive regulation of transcription by RNA polymerase II	1	14.9×	0.077	PHF8
regulation of transcription by RNA polymerase II	1	11.7×	0.086	PHF8

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
PHF8	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
PHF8	26	Binding:26

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
PHF8	1.14.11.65, 1.14.18.B1	[histone H3]-dimethyl-L-lysine9 demethylase,

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	PHF8

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
PHF8	26	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.