FAM78A

Summary

FAM78A (family with sequence similarity 78 member A, HGNC:25465) is a protein-coding gene on chromosome 9q34.13, encoding Protein FAM78A (Q5JUQ0).

At a glance

• Clinical variants (ClinVar): 51 total — 1 pathogenic
• MANE Select transcript: NM_033387

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25465
Approved symbol	FAM78A
Name	family with sequence similarity 78 member A
Location	9q34.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ00024
Ensembl gene	ENSG00000126882
Ensembl biotype	protein_coding
Entrez	286336

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000247295, ENST00000372269, ENST00000372271, ENST00000464831, ENST00000704762

RefSeq mRNA: 9 — MANE Select: NM_033387 NM_001399459, NM_001400581, NM_001400582, NM_001400583, NM_001400584, NM_001400588, NM_001400592, NM_001400594, NM_033387

CCDS: CCDS6941, CCDS94514

Canonical transcript exons

ENST00000372271 — 2 exons

Exon	Start	End
ENSE00001334024	131275857	131276510
ENSE00003850617	131258078	131261350

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 94.35.

FANTOM5 (CAGE): breadth broad, TPM avg 4.1586 / max 80.8415, expressed in 565 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
102826	1.0745	344
102827	0.9941	329
102824	0.6231	256
102820	0.4845	189
102825	0.4810	246
102828	0.4097	201
102821	0.0917	52

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	94.35	gold quality
thymus	UBERON:0002370	91.63	gold quality
vastus lateralis	UBERON:0001379	91.60	gold quality
leukocyte	CL:0000738	91.24	gold quality
left ventricle myocardium	UBERON:0006566	91.16	gold quality
quadriceps femoris	UBERON:0001377	91.06	gold quality
apex of heart	UBERON:0002098	91.05	gold quality
cardiac muscle of right atrium	UBERON:0003379	90.93	gold quality
monocyte	CL:0000576	90.88	gold quality
myocardium	UBERON:0002349	90.58	gold quality
blood	UBERON:0000178	90.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	89.71	gold quality
biceps brachii	UBERON:0001507	89.28	gold quality
skeletal muscle tissue	UBERON:0001134	88.18	gold quality
cardiac atrium	UBERON:0002081	87.94	gold quality
lymph node	UBERON:0000029	87.83	gold quality
right atrium auricular region	UBERON:0006631	87.64	gold quality
left testis	UBERON:0004533	87.51	gold quality
right testis	UBERON:0004534	87.29	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.76	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	86.67	gold quality
muscle tissue	UBERON:0002385	86.53	gold quality
heart left ventricle	UBERON:0002084	86.44	gold quality
cardiac ventricle	UBERON:0002082	86.38	gold quality
spleen	UBERON:0002106	86.16	gold quality
trabecular bone tissue	UBERON:0002483	85.82	gold quality
skeletal muscle organ	UBERON:0014892	85.00	gold quality
testis	UBERON:0000473	84.74	gold quality
heart	UBERON:0000948	84.43	gold quality
vermiform appendix	UBERON:0001154	83.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

175 targeting FAM78A, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-6755-5P	99.95	65.59	464
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam78ab	ENSDARG00000088222
mus_musculus	Fam78a	ENSMUSG00000050592
rattus_norvegicus	Fam78a	ENSRNOG00000023352

Paralogs (1): FAM78B (ENSG00000188859)

Protein

Protein identifiers

Protein FAM78A — Q5JUQ0 (reviewed: Q5JUQ0)

All UniProt accessions (3): Q5JUQ0, Q5JUQ1, Q5JUQ2

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM78 family.

RefSeq proteins (9): NP_001386388, NP_001387510, NP_001387511, NP_001387512, NP_001387513, NP_001387517, NP_001387521, NP_001387523, NP_203745* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029638	FAM78	Family

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JUQ0-F1	89.34	0.86

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 230 (showing top): RNGTGGGC_UNKNOWN, BENPORATH_ES_WITH_H3K27ME3, PAX4_01, TGCACTT_MIR519C_MIR519B_MIR519A, AP2_Q3, ATF1_Q6, TGACATY_UNKNOWN, ATF3_Q6, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, AFP1_Q6, AACTTT_UNKNOWN, MAF_Q6, RYTTCCTG_ETS2_B, CDPCR3HD_01, TGCCTTA_MIR124A

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

688 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM78A	ZNF540	Q8NDQ6	571
FAM78A	ZNF671	Q8TAW3	479
FAM78A	RIMS4	Q9H426	473
FAM78A	PCDHAC1	Q9H158	450
FAM78A	ARHGAP30	Q7Z6I6	449
FAM78A	ALKAL1	Q6UXT8	447
FAM78A	ZNF154	Q13106	447
FAM78A	PRAC1	Q96KF2	432
FAM78A	AP2A1	O95782	392
FAM78A	RASL11A	Q6T310	386
FAM78A	SLC35G1	Q2M3R5	376
FAM78A	ARL2	P36404	375
FAM78A	KHDRBS2	Q5VWX1	375
FAM78A	KCNK13	Q9HB14	369
FAM78A	GJD4	Q96KN9	359

IntAct

15 interactions, top by confidence:

A	B	Type	Score
FAM78A		psi-mi:“MI:0915”(physical association)	0.560
FAM78A	PMP22	psi-mi:“MI:0915”(physical association)	0.560
FAM78A	PEX26	psi-mi:“MI:0915”(physical association)	0.560
HTT	FAM78A	psi-mi:“MI:0915”(physical association)	0.560
FAM78A	ADD3	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (7): ASNS (Affinity Capture-MS), ADD1 (Affinity Capture-MS), ADD3 (Affinity Capture-MS), ADD3 (Affinity Capture-MS), FAM78A (Affinity Capture-RNA), ADD3 (Affinity Capture-MS), FAM78A (Affinity Capture-RNA)

ESM2 similar proteins: A0A1V6NYM5, A3RM21, A4QJT6, A4UHQ0, A4UHQ5, A9QC92, B4SCX8, B7INA4, C4QGM3, H6QW39, O48397, O74358, O92551, P04028, P05074, P05673, P06942, P06944, P08671, P0C571, P0DOF2, P13844, P15200, P16287, P18611, P20402, P25223, P25224, P31823, P41358, P50624, Q06RC6, Q0GBY2, Q32RZ2, Q5BK64, Q5JUQ0, Q5UPI4, Q5VKP4, Q66T63, Q6JAM6

Diamond homologs: Q5JUQ0, Q5VT40, Q8BQN5, Q8C552

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	44
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
59909	GRCh38/hg38 9q34.13(chr9:131261516-131741175)x3	Pathogenic

SpliceAI

233 predictions. Top by Δscore:

Variant	Effect	Δscore
9:131261351:C:CC	acceptor_gain	1.0000
9:131275855:A:AC	donor_gain	1.0000
9:131275855:ACATG:A	donor_gain	1.0000
9:131275856:C:CC	donor_gain	1.0000
9:131275856:CATG:C	donor_gain	1.0000
9:131275856:CATGC:C	donor_gain	1.0000
9:131261350:CCTG:C	acceptor_loss	0.9900
9:131261351:CTGAG:C	acceptor_loss	0.9900
9:131261352:T:C	acceptor_loss	0.9900
9:131275849:GTAC:G	donor_loss	0.9900
9:131275851:A:AC	donor_gain	0.9900
9:131275852:C:CC	donor_gain	0.9900
9:131275853:TCAC:T	donor_loss	0.9900
9:131275854:CA:C	donor_loss	0.9900
9:131275855:ACAT:A	donor_loss	0.9900
9:131275856:C:A	donor_loss	0.9900
9:131275873:A:AC	donor_gain	0.9900
9:131275874:C:CC	donor_gain	0.9900
9:131275859:G:A	donor_gain	0.9800
9:131261346:TGGAC:T	acceptor_gain	0.9700
9:131275918:C:CT	donor_gain	0.9700
9:131275919:T:TT	donor_gain	0.9700
9:131275955:C:CT	donor_gain	0.9700
9:131261347:GGACC:G	acceptor_gain	0.9600
9:131261349:ACCTG:A	acceptor_gain	0.9600
9:131275852:CTCA:C	donor_gain	0.9600
9:131275856:CAT:C	donor_gain	0.9600
9:131275868:G:A	donor_gain	0.9600
9:131275954:C:CT	donor_gain	0.9600
9:131261349:AC:A	acceptor_gain	0.9500

AlphaMissense

1878 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:131260871:C:G	R268P	1.000
9:131260873:C:A	W267C	1.000
9:131260873:C:G	W267C	1.000
9:131260874:C:G	W267S	1.000
9:131260875:A:G	W267R	1.000
9:131260875:A:T	W267R	1.000
9:131260880:A:G	L265P	1.000
9:131260880:A:T	L265H	1.000
9:131260885:C:A	Q263H	1.000
9:131260885:C:G	Q263H	1.000
9:131260890:C:G	A262P	1.000
9:131260894:G:C	N260K	1.000
9:131260894:G:T	N260K	1.000
9:131260896:T:C	N260D	1.000
9:131260898:G:T	A259D	1.000
9:131260955:G:T	P240H	1.000
9:131260992:G:T	R228S	1.000
9:131261030:A:G	L215P	1.000
9:131261041:C:A	W211C	1.000
9:131261041:C:G	W211C	1.000
9:131261042:C:G	W211S	1.000
9:131261043:A:G	W211R	1.000
9:131261043:A:T	W211R	1.000
9:131261090:G:T	A195D	1.000
9:131261096:A:G	L193P	1.000
9:131261100:A:G	W192R	1.000
9:131261100:A:T	W192R	1.000
9:131261107:G:C	F189L	1.000
9:131261107:G:T	F189L	1.000
9:131261108:A:C	F189C	1.000

dbSNP variants (sampled 300 via entrez): RS1000071474 (9:131275577 T>C), RS1000088752 (9:131270828 G>C), RS1000117219 (9:131269863 A>G), RS1000217994 (9:131264300 G>T), RS1000301991 (9:131266643 A>G), RS1000361636 (9:131261019 C>A), RS1000377806 (9:131276725 G>A,T), RS1000447412 (9:131258941 C>A), RS1000567899 (9:131267324 G>A), RS1000631306 (9:131266442 A>C), RS1000853723 (9:131280336 C>T), RS1000880325 (9:131259160 G>A), RS1000963592 (9:131274122 C>G), RS1001041428 (9:131267583 T>C), RS1001055496 (9:131274342 C>G,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

0 associations (top):

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

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects cotreatment, increases expression, affects expression	5
entinostat	increases expression, affects cotreatment	2
Nickel	decreases expression, increases expression	2
bisphenol F	affects cotreatment, increases expression	1
aminomethylphosphonic acid (AMPA)	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
licochalcone B	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants, Occupational	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression	1
Cisplatin	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Estradiol	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Triclosan	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	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