FAM47A

Summary

FAM47A (family with sequence similarity 47 member A, HGNC:29962) is a protein-coding gene on chromosome Xp21.1, encoding Protein FAM47A (Q5JRC9).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 121 total
• MANE Select transcript: NM_203408

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29962
Approved symbol	FAM47A
Name	family with sequence similarity 47 member A
Location	Xp21.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC27003
Ensembl gene	ENSG00000185448
Ensembl biotype	protein_coding
Entrez	158724

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000346193

RefSeq mRNA: 1 — MANE Select: NM_203408 NM_203408

CCDS: CCDS43926

Canonical transcript exons

ENST00000346193 — 1 exons

Exon	Start	End
ENSE00001310051	34129752	34132314

Expression profiles

Bgee: expression breadth tissue_specific, 8 present calls, max score 76.84.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0119 / max 6.7663, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
198862	0.0119	4

Top tissues by expression

252 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	76.84	silver quality
adult organism	UBERON:0007023	57.34	silver quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
epithelial cell of pancreas	CL:0000083	53.71	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
testis	UBERON:0000473	52.93	gold quality
pancreatic ductal cell	CL:0002079	52.27	silver quality
left testis	UBERON:0004533	52.17	gold quality
tibialis anterior	UBERON:0001385	51.80	silver quality
right testis	UBERON:0004534	50.58	gold quality
myocardium	UBERON:0002349	50.25	gold quality
deltoid	UBERON:0001476	48.19	gold quality
ileal mucosa	UBERON:0000331	47.71	silver quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
quadriceps femoris	UBERON:0001377	46.32	gold quality
vastus lateralis	UBERON:0001379	45.40	gold quality
buccal mucosa cell	CL:0002336	43.80	gold quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
skeletal muscle tissue	UBERON:0001134	43.11	gold quality
muscle tissue	UBERON:0002385	42.84	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
colonic epithelium	UBERON:0000397	41.67	gold quality
calcaneal tendon	UBERON:0003701	41.45	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
tendon	UBERON:0000043	40.85	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting FAM47A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-6853-3P	99.36	70.79	1558
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-4712-3P	98.52	65.39	822
HSA-MIR-744-3P	97.99	67.76	637
HSA-MIR-4678	97.59	68.31	902
HSA-MIR-6501-5P	97.41	68.24	712
HSA-MIR-6509-5P	97.39	68.27	969
HSA-MIR-6869-5P	97.17	67.06	634
HSA-MIR-331-5P	96.59	67.94	705
HSA-MIR-5681B	94.82	69.30	514

Literature-anchored findings (GeneRIF, showing 1)

• Includes the identification of a phosphopeptide from this protein. (PMID:17924679)

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
danio_rerio	fmn2b	ENSDARG00000061778
danio_rerio	fhdc2	ENSDARG00000099767
drosophila_melanogaster	capu	FBGN0000256
drosophila_melanogaster	dia	FBGN0011202
drosophila_melanogaster	form3	FBGN0053556
drosophila_melanogaster	Frl	FBGN0267795
caenorhabditis_elegans		WBGENE00000872
caenorhabditis_elegans	fhod-1	WBGENE00016735
caenorhabditis_elegans		WBGENE00018976
caenorhabditis_elegans		WBGENE00019030
caenorhabditis_elegans	sydn-1	WBGENE00021473
caenorhabditis_elegans		WBGENE00021698

Paralogs (18): DAAM1 (ENSG00000100592), FNBP4 (ENSG00000109920), DIAPH1 (ENSG00000131504), FHOD3 (ENSG00000134775), FHOD1 (ENSG00000135723), FHDC1 (ENSG00000137460), DIAPH3 (ENSG00000139734), DAAM2 (ENSG00000146122), DIAPH2 (ENSG00000147202), FMN2 (ENSG00000155816), FMNL2 (ENSG00000157827), FMNL3 (ENSG00000161791), FMNL1 (ENSG00000184922), SHTN1 (ENSG00000187164), FAM47B (ENSG00000189132), FAM47C (ENSG00000198173), INF2 (ENSG00000203485), GRID2IP (ENSG00000215045)

Protein

Protein identifiers

Protein FAM47A — Q5JRC9 (reviewed: Q5JRC9)

All UniProt accessions (1): Q5JRC9

UniProt curated annotations — full annotation on UniProt →

Polymorphism. The repeat encompassing Pro-495 to Glu-507 may be polymorphic.

Similarity. Belongs to the FAM47 family.

RefSeq proteins (1): NP_981953* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032743	FAM47	Family

Pfam: PF14642

UniProt features (13 total): sequence variant 5, compositionally biased region 4, region of interest 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JRC9-F1	47.52	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): chrXp21, GSE14386_UNTREATED_VS_IFNA_TREATED_ACT_PBMC_MS_PATIENT_UP, MIR6853_3P, MIR6501_5P, MIR744_3P, MIR6869_5P, GSE15659_NAIVE_VS_PTPRC_NEG_CD4_TCELL_UP, GSE15659_NAIVE_CD4_TCELL_VS_RESTING_TREG_UP, GSE15659_NAIVE_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_UP, GSE15659_NAIVE_CD4_TCELL_VS_ACTIVATED_TREG_UP, GSE15659_CD45RA_NEG_CD4_TCELL_VS_RESTING_TREG_UP, GSE15659_CD45RA_NEG_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_UP, GSE15659_CD45RA_NEG_CD4_TCELL_VS_ACTIVATED_TREG_UP, GSE15659_RESTING_TREG_VS_NONSUPPRESSIVE_TCELL_UP, GSE15659_RESTING_VS_ACTIVATED_TREG_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

448 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM47A	UBN2	Q6ZU65	505
FAM47A	PHF3	Q92576	447
FAM47A	NEXMIF	Q5QGS0	446
FAM47A	DIP2C	Q9Y2E4	446
FAM47A	NBPF20	P0DPF2	419
FAM47A	OR4Q3	Q8NH05	376
FAM47A	TAF6	P49848	372
FAM47A	SRSF11	Q05519	372
FAM47A	CLASP1	Q7Z460	370
FAM47A	QTMAN	Q4AE62	369
FAM47A	ZCCHC2	Q9C0B9	368
FAM47A	MAGEB1	P43366	367
FAM47A	AGAP2	Q99490	355
FAM47A	CNOT3	O75175	326
FAM47A	FRMPD4	Q14CM0	324

IntAct

4 interactions, top by confidence:

A	B	Type	Score
FAM47A	NCK2	psi-mi:“MI:0915”(physical association)	0.560
NCK2	FAM47A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): FAM47A (Affinity Capture-MS), FAM47A (Two-hybrid)

ESM2 similar proteins: A0A1B0GUY1, A6NJ88, A6QL64, B3KS81, E9Q6E9, O43493, O48582, O77733, P04279, P0C7A4, P0C7A5, P0CV57, P0DKJ7, P10322, P16225, P48997, P48998, Q02383, Q06990, Q08AG5, Q0ZNK1, Q5JPF3, Q5JRC9, Q5SRN2, Q5U7M7, Q5U7M8, Q5U7M9, Q5U7N0, Q5U7N1, Q5U7N3, Q5U7N4, Q5XHX6, Q659K0, Q6AYN3, Q6JHY2, Q6P902, Q6SJ82, Q6X2M3, Q6XPR3, Q80Y39

Diamond homologs: A6NHR8, Q5JRC9, Q6ZV65, Q8NA70, Q5HY64

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

121 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	91
Likely benign	19
Benign	7

Top pathogenic / likely-pathogenic (0)

SpliceAI

5 predictions. Top by Δscore:

Variant	Effect	Δscore
X:34131695:G:GT	acceptor_gain	0.3400
X:34131458:T:TA	donor_gain	0.2900
X:34131465:T:TA	donor_gain	0.2500
X:34131353:G:GT	donor_gain	0.2200
X:34131394:T:C	donor_gain	0.2200

AlphaMissense

5136 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:34130053:G:C	F742L	0.993
X:34130053:G:T	F742L	0.993
X:34130055:A:G	F742L	0.993
X:34130059:C:A	K740N	0.990
X:34130059:C:G	K740N	0.990
X:34130446:G:C	F611L	0.988
X:34130446:G:T	F611L	0.988
X:34130448:A:G	F611L	0.988
X:34130062:A:C	F739L	0.987
X:34130062:A:T	F739L	0.987
X:34130064:A:G	F739L	0.987
X:34130063:A:G	F739S	0.985
X:34129992:A:G	W763R	0.981
X:34129992:A:T	W763R	0.981
X:34130005:A:C	F758L	0.981
X:34130005:A:T	F758L	0.981
X:34130007:A:G	F758L	0.981
X:34130054:A:G	F742S	0.981
X:34130187:A:G	W698R	0.981
X:34130187:A:T	W698R	0.981
X:34130051:A:T	I743N	0.978
X:34132129:A:C	F50L	0.974
X:34132129:A:T	F50L	0.974
X:34132131:A:G	F50L	0.974
X:34130386:A:C	F631L	0.970
X:34130386:A:T	F631L	0.970
X:34130388:A:G	F631L	0.970
X:34130447:A:G	F611S	0.970
X:34129990:C:A	W763C	0.969
X:34129990:C:G	W763C	0.969

dbSNP variants (sampled 300 via entrez): RS1001806022 (X:34132697 A>G), RS1002043248 (X:34130487 A>G), RS1002068433 (X:34132365 G>A,C), RS1003423114 (X:34132404 G>A), RS1003764206 (X:34131796 G>A), RS1006476231 (X:34134119 A>T), RS1008326859 (X:34133462 T>G), RS1008876546 (X:34129795 A>G), RS1009075519 (X:34131403 C>T), RS1009673530 (X:34130497 G>A), RS1009729142 (X:34129708 A>C), RS1009931354 (X:34132284 C>G,T), RS1010459857 (X:34131728 C>A,T), RS1010678991 (X:34133320 C>G,T), RS1010730047 (X:34132431 G>A,C,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): intellectual disability (MONDO:0001071)

Orphanet (1): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002127_25	Periodontitis (Mean PAL)	8.000000e-06
GCST006442_455	Educational attainment (years of education)	6.000000e-10
GCST006442_457	Educational attainment (years of education)	5.000000e-14

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004784	self reported educational attainment

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

197 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT05657860	PHASE4	COMPLETED	Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479	PHASE4	RECRUITING	Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829	PHASE4	WITHDRAWN	Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198	PHASE4	NOT_YET_RECRUITING	Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736	PHASE3	COMPLETED	Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302	PHASE2	COMPLETED	Down Syndrome Memantine Follow-up Study
NCT03862950	PHASE2	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226	PHASE2	UNKNOWN	Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856	PHASE2	COMPLETED	Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320	PHASE1	COMPLETED	Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361	PHASE1	ENROLLING_BY_INVITATION	Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764	PHASE1	COMPLETED	Use of MRI and cTBS for Catatonia in Autism
NCT06586827	PHASE1	COMPLETED	Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940	PHASE1	NOT_YET_RECRUITING	Escalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476	PHASE2/PHASE3	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796	PHASE1/PHASE2	COMPLETED	Effects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672	EARLY_PHASE1	RECRUITING	Clinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948	Not specified	COMPLETED	Healthy Lifestyles for People With Intellectual Disabilities
NCT01087320	Not specified	RECRUITING	Genome Medical Sequencing for Gene Discovery
NCT01652963	Not specified	UNKNOWN	Picture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395	Not specified	COMPLETED	Mental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554	Not specified	COMPLETED	Research and Characterization of New Genes Involved in Intellectual Disability
NCT01915381	Not specified	COMPLETED	Improving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623	Not specified	COMPLETED	Pivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773	Not specified	COMPLETED	Support Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849	Not specified	COMPLETED	Inter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041	Not specified	COMPLETED	Sedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438	Not specified	COMPLETED	Establishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761	Not specified	COMPLETED	Apparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420	Not specified	ACTIVE_NOT_RECRUITING	Mapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459	Not specified	ACTIVE_NOT_RECRUITING	Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081	Not specified	COMPLETED	Development and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502	Not specified	COMPLETED	Enhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277	Not specified	COMPLETED	Diabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754	Not specified	COMPLETED	Weight Management for Adolescents With IDD
NCT02591446	Not specified	COMPLETED	Transcranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868	Not specified	COMPLETED	Evaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394	Not specified	UNKNOWN	FCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614	Not specified	COMPLETED	Psychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405	Not specified	COMPLETED	TMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders