FAM204A

Summary

FAM204A (family with sequence similarity 204 member A, HGNC:25794) is a protein-coding gene on chromosome 10q26.11, encoding Protein FAM204A (Q9H8W3).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 41 total
• MANE Select transcript: NM_022063

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25794
Approved symbol	FAM204A
Name	family with sequence similarity 204 member A
Location	10q26.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13188, bA319I23.1
Ensembl gene	ENSG00000165669
Ensembl biotype	protein_coding
Entrez	63877

Gene structure

Transcript identifiers

Ensembl transcripts: 33 — 26 protein_coding, 3 protein_coding_CDS_not_defined, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000369170, ENST00000369172, ENST00000369183, ENST00000452252, ENST00000467890, ENST00000469758, ENST00000470476, ENST00000487269, ENST00000490048, ENST00000491416, ENST00000885074, ENST00000885075, ENST00000885076, ENST00000885077, ENST00000885078, ENST00000885079, ENST00000885080, ENST00000885081, ENST00000885082, ENST00000885083, ENST00000885084, ENST00000885085, ENST00000885086, ENST00000885087, ENST00000885088, ENST00000935478, ENST00000935479, ENST00000935480, ENST00000935481, ENST00000942972, ENST00000942973, ENST00000942974, ENST00000942975

RefSeq mRNA: 2 — MANE Select: NM_022063 NM_001134672, NM_022063

CCDS: CCDS7605

Canonical transcript exons

ENST00000369183 — 9 exons

Exon	Start	End
ENSE00001362266	118341727	118341927
ENSE00001448969	118297925	118310908
ENSE00003289621	118335396	118335426
ENSE00003565182	118311207	118311313
ENSE00003639330	118336182	118336423
ENSE00003648091	118326154	118326243
ENSE00003663616	118335554	118335641
ENSE00003790791	118335114	118335213
ENSE00003841347	118342270	118342324

Expression profiles

Bgee: expression breadth ubiquitous, 266 present calls, max score 98.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.9371 / max 753.4331, expressed in 1801 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
111635	32.9371	1801

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	98.85	gold quality
monocyte	CL:0000576	96.92	gold quality
mononuclear cell	CL:0000842	96.49	gold quality
leukocyte	CL:0000738	96.26	gold quality
left testis	UBERON:0004533	95.42	gold quality
right testis	UBERON:0004534	95.20	gold quality
tendon	UBERON:0000043	95.01	gold quality
ventricular zone	UBERON:0003053	94.85	gold quality
tibial artery	UBERON:0007610	94.63	gold quality
gall bladder	UBERON:0002110	94.62	gold quality
popliteal artery	UBERON:0002250	94.62	gold quality
testis	UBERON:0000473	94.52	gold quality
rectum	UBERON:0001052	94.49	gold quality
ganglionic eminence	UBERON:0004023	94.37	gold quality
mucosa of stomach	UBERON:0001199	94.15	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.92	gold quality
cortical plate	UBERON:0005343	93.86	gold quality
prefrontal cortex	UBERON:0000451	93.85	gold quality
aorta	UBERON:0000947	93.85	gold quality
body of pancreas	UBERON:0001150	93.79	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.74	gold quality
gastrocnemius	UBERON:0001388	93.72	gold quality
lower esophagus	UBERON:0013473	93.72	gold quality
left coronary artery	UBERON:0001626	93.62	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.62	gold quality
subcutaneous adipose tissue	UBERON:0002190	93.55	gold quality
caudate nucleus	UBERON:0001873	93.51	gold quality
saphenous vein	UBERON:0007318	93.42	gold quality
anterior cingulate cortex	UBERON:0009835	93.40	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.40	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.84
E-GEOD-100618	no	638.87
E-MTAB-6142	no	128.88
E-HCAD-13	no	2.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

86 targeting FAM204A, 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-3613-3P	100.00	76.36	7965
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-7856-5P	99.75	69.99	2901

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam204a	ENSDARG00000039699
mus_musculus	Fam204a	ENSMUSG00000057858
rattus_norvegicus	Fam204a	ENSRNOG00000009830

Protein

Protein identifiers

Protein FAM204A — Q9H8W3 (reviewed: Q9H8W3)

All UniProt accessions (3): Q9H8W3, F2Z2Y3, Q5T374

RefSeq proteins (2): NP_001128144, NP_071346* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037690	FAM204A	Family

UniProt features (8 total): compositionally biased region 3, sequence conflict 2, chain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H8W3-F1	71.34	0.35

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 102 (showing top): MYAATNNNNNNNGGC_UNKNOWN, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN, NUYTTEN_EZH2_TARGETS_DN, JOHNSTONE_PARVB_TARGETS_3_DN, NFY_Q6_01, RAO_BOUND_BY_SALL4_ISOFORM_B, DCA_UP.V1_DN, ASH1L_TARGET_GENES, CIITA_TARGET_GENES, NFE2L1_TARGET_GENES, TAF9B_TARGET_GENES, ZIM3_TARGET_GENES, ZNF512B_TARGET_GENES, MIR616_5P, MIR371B_5P

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

376 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM204A	TMEM184C	Q9NVA4	618
FAM204A	HSF2	Q03933	539
FAM204A	MFAP3L	O75121	528
FAM204A	RAB11FIP2	Q7L804	477
FAM204A	C7orf25	Q9BPX7	477
FAM204A	CHCHD3	Q9NX63	456
FAM204A	FAM133B	Q5BKY9	437
FAM204A	ANKRD40	Q6AI12	435
FAM204A	NAA10	P41227	434
FAM204A	FAM110B	Q8TC76	431
FAM204A	TMEM179	Q6ZVK1	424
FAM204A	SMU1	Q2TAY7	410
FAM204A	HAUS8	Q9BT25	386
FAM204A	EXOC4	Q96A65	366
FAM204A	CLIP3	Q96DZ5	348

IntAct

24 interactions, top by confidence:

A	B	Type	Score
SMYD1	FAM204A	psi-mi:“MI:0915”(physical association)	0.670
FAM204A	SMYD1	psi-mi:“MI:0915”(physical association)	0.670
FHL2	FAM204A	psi-mi:“MI:0915”(physical association)	0.560
KDM1A	FAM204A	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	FAM204A	psi-mi:“MI:0915”(physical association)	0.560
FAM177A1	SLC27A2	psi-mi:“MI:0914”(association)	0.530
FXYD1	GCHFR	psi-mi:“MI:0914”(association)	0.530
CCDC60	DCP1B	psi-mi:“MI:0914”(association)	0.530
CCDC60	ZNF593	psi-mi:“MI:0914”(association)	0.350
S100A6	VWA8	psi-mi:“MI:0914”(association)	0.350
H2AJ	WDR46	psi-mi:“MI:0914”(association)	0.350
SERF2	WDR46	psi-mi:“MI:0914”(association)	0.350
CRCP	SRC	psi-mi:“MI:0914”(association)	0.350
PLGRKT	VPS13C	psi-mi:“MI:0914”(association)	0.350
SPANXN2	FAM204A	psi-mi:“MI:0915”(physical association)	0.000
SMYD1	FAM204A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (32): FAM204A (Affinity Capture-MS), FAM204A (Affinity Capture-MS), HAT1 (Affinity Capture-MS), KPNB1 (Affinity Capture-MS), NPEPPS (Affinity Capture-MS), KPNA2 (Affinity Capture-MS), KPNA3 (Affinity Capture-MS), COPG1 (Affinity Capture-MS), FAM204A (Affinity Capture-MS), FAM204A (Affinity Capture-MS), FAM204A (Affinity Capture-MS), FAM204A (Two-hybrid), FAM204A (Two-hybrid), FAM204A (Two-hybrid), SPANXN2 (Two-hybrid)

ESM2 similar proteins: A0AUP1, A4II15, A7MCB7, E1C760, F6RRD7, F7AEX0, P14629, P78316, Q1L8X2, Q28DG8, Q2IA00, Q3T071, Q3U155, Q3ZCI6, Q4R6T7, Q4R8R3, Q4R8V8, Q4V7N4, Q5PQS7, Q5R939, Q5RA37, Q5XI65, Q5ZIH9, Q5ZIM6, Q6DFL5, Q6IEG0, Q6PBE2, Q6PII3, Q7SYB2, Q7ZXA8, Q80VN0, Q8C6C7, Q8C9J3, Q8CIL4, Q8IXW5, Q8R3N1, Q8R3N6, Q8VYD3, Q93VM9, Q95JM8

Diamond homologs: Q3ZCI6, Q5R939, Q8C6C7, Q9H8W3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1757 predictions. Top by Δscore:

Variant	Effect	Δscore
10:118309870:A:AC	donor_gain	1.0000
10:118311199:AAACT:A	donor_loss	1.0000
10:118311200:AACTC:A	donor_loss	1.0000
10:118311201:ACTC:A	donor_loss	1.0000
10:118311202:CTCAC:C	donor_loss	1.0000
10:118311203:TCACC:T	donor_loss	1.0000
10:118311204:CACC:C	donor_loss	1.0000
10:118311205:A:C	donor_loss	1.0000
10:118311205:AC:A	donor_gain	1.0000
10:118311205:ACC:A	donor_gain	1.0000
10:118311205:ACCC:A	donor_gain	1.0000
10:118311206:C:CG	donor_loss	1.0000
10:118311206:CC:C	donor_gain	1.0000
10:118311206:CCC:C	donor_gain	1.0000
10:118311206:CCCC:C	donor_gain	1.0000
10:118311309:CCAAG:C	acceptor_gain	1.0000
10:118311310:CAAG:C	acceptor_gain	1.0000
10:118311310:CAAGC:C	acceptor_gain	1.0000
10:118311311:AAG:A	acceptor_gain	1.0000
10:118311312:AG:A	acceptor_gain	1.0000
10:118311312:AGCTA:A	acceptor_loss	1.0000
10:118311313:GCT:G	acceptor_loss	1.0000
10:118311314:C:CC	acceptor_gain	1.0000
10:118311315:T:C	acceptor_loss	1.0000
10:118311321:T:C	acceptor_gain	1.0000
10:118311321:T:TC	acceptor_gain	1.0000
10:118326149:CTCA:C	donor_loss	1.0000
10:118326150:TCA:T	donor_loss	1.0000
10:118326151:CA:C	donor_loss	1.0000
10:118326152:A:AC	donor_gain	1.0000

AlphaMissense

1551 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:118310887:C:A	W224C	1.000
10:118310887:C:G	W224C	1.000
10:118310889:A:G	W224R	1.000
10:118310889:A:T	W224R	1.000
10:118310878:T:A	K227N	0.999
10:118310878:T:G	K227N	0.999
10:118310888:C:G	W224S	0.999
10:118310905:A:C	F218L	0.999
10:118310905:A:T	F218L	0.999
10:118310907:A:G	F218L	0.999
10:118311209:C:A	W216C	0.999
10:118311209:C:G	W216C	0.999
10:118311211:A:G	W216R	0.999
10:118311211:A:T	W216R	0.999
10:118310869:C:A	M230I	0.998
10:118310869:C:G	M230I	0.998
10:118310869:C:T	M230I	0.998
10:118310879:T:A	K227I	0.998
10:118310890:T:A	R223S	0.998
10:118310890:T:G	R223S	0.998
10:118310896:C:A	K221N	0.998
10:118310896:C:G	K221N	0.998
10:118311292:C:G	A189P	0.998
10:118310868:C:G	G231R	0.997
10:118310868:C:T	G231R	0.997
10:118310875:G:C	S228R	0.997
10:118310875:G:T	S228R	0.997
10:118310877:T:G	S228R	0.997
10:118310880:T:G	K227Q	0.997
10:118310891:C:G	R223T	0.997

dbSNP variants (sampled 300 via entrez): RS1000021509 (10:118299453 C>A,T), RS1000105366 (10:118299723 T>C), RS1000115220 (10:118299447 T>A,C), RS1000278370 (10:118316720 G>A), RS1000297430 (10:118336618 A>C), RS1000309289 (10:118316366 C>T), RS1000321600 (10:118305619 G>T), RS1000428657 (10:118313558 T>C,G), RS1000477780 (10:118299242 G>C), RS1000600448 (10:118304562 C>T), RS1000610891 (10:118318376 C>T), RS1000645067 (10:118317999 C>A), RS1000668244 (10:118312421 C>T), RS1000670612 (10:118305909 T>C), RS1000827708 (10:118325170 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006858_1	Leisure-time exercise behaviour (age-stratified)	1.000000e-07
GCST012322_45	Triglyceride levels x SSRI defined daily dose interaction in schizophrenia or bipolar disorder	1.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0000483	exercise
EFO:0004530	triglyceride measurement
EFO:0005658	response to selective serotonin reuptake inhibitor

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Valproic Acid	affects expression, increases expression	2
dicrotophos	decreases expression	1
afimoxifene	decreases expression, decreases reaction	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	decreases expression	1
Carbamazepine	affects expression	1
Estrogens	decreases expression, decreases reaction	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Zinc	decreases expression	1
Cyclosporine	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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