FAM89A

Summary

FAM89A (family with sequence similarity 89 member A, HGNC:25057) is a protein-coding gene on chromosome 1q42.2, encoding Protein FAM89A (Q96GI7).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_198552

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25057
Approved symbol	FAM89A
Name	family with sequence similarity 89 member A
Location	1q42.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC15887
Ensembl gene	ENSG00000182118
Ensembl biotype	protein_coding
Entrez	375061

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000366654, ENST00000466258, ENST00000494111, ENST00000951728, ENST00000951729, ENST00000951730

RefSeq mRNA: 1 — MANE Select: NM_198552 NM_198552

CCDS: CCDS1590

Canonical transcript exons

ENST00000366654 — 2 exons

Exon	Start	End
ENSE00001442261	231018958	231020126
ENSE00001442262	231039921	231040254

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 96.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.1182 / max 114.2238, expressed in 1472 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
17970	5.5789	1461
17969	0.5393	262

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
placenta	UBERON:0001987	96.93	gold quality
omental fat pad	UBERON:0010414	93.27	gold quality
adipose tissue	UBERON:0001013	92.60	gold quality
subcutaneous adipose tissue	UBERON:0002190	91.95	gold quality
right lung	UBERON:0002167	89.67	gold quality
substantia nigra	UBERON:0002038	89.37	gold quality
skin of leg	UBERON:0001511	89.29	gold quality
hypothalamus	UBERON:0001898	88.62	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	88.61	gold quality
zone of skin	UBERON:0000014	88.48	gold quality
skin of abdomen	UBERON:0001416	87.55	gold quality
left adrenal gland	UBERON:0001234	87.02	gold quality
left adrenal gland cortex	UBERON:0035825	86.96	gold quality
upper lobe of left lung	UBERON:0008952	86.31	gold quality
right adrenal gland cortex	UBERON:0035827	86.25	gold quality
thoracic mammary gland	UBERON:0005200	86.18	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.80	gold quality
adrenal gland	UBERON:0002369	85.41	gold quality
right adrenal gland	UBERON:0001233	85.11	gold quality
lung	UBERON:0002048	84.80	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.66	gold quality
spleen	UBERON:0002106	84.30	gold quality
amygdala	UBERON:0001876	83.81	gold quality
temporal lobe	UBERON:0001871	83.63	gold quality
nucleus accumbens	UBERON:0001882	83.53	gold quality
Ammon’s horn	UBERON:0001954	83.36	gold quality
caudate nucleus	UBERON:0001873	82.58	gold quality
adult mammalian kidney	UBERON:0000082	82.51	gold quality
stromal cell of endometrium	CL:0002255	81.69	gold quality
endocervix	UBERON:0000458	80.90	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-5	yes	769.12
E-MTAB-9388	yes	564.85
E-MTAB-10485	yes	445.57
E-GEOD-109979	yes	43.65
E-ANND-3	yes	5.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting FAM89A, 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-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-548AI	99.69	69.24	1494
HSA-MIR-548BA	99.69	69.14	1514

Literature-anchored findings (GeneRIF, showing 2)

• A qPCR expression assay of IFI44L gene differentiates viral from bacterial infections in febrile children. (PMID:31409879)
• Transcriptome-wide association study reveals two genes that influence mismatch negativity. (PMID:33730571)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam89a	ENSDARG00000079979
mus_musculus	Fam89a	ENSMUSG00000043068
rattus_norvegicus	Fam89a	ENSRNOG00000019022
drosophila_melanogaster	CG31038	FBGN0051038
drosophila_melanogaster	lmgB	FBGN0085470

Paralogs (2): TRANK1 (ENSG00000168016), FAM89B (ENSG00000176973)

Protein

Protein identifiers

Protein FAM89A — Q96GI7 (reviewed: Q96GI7)

All UniProt accessions (1): Q96GI7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM89 family.

RefSeq proteins (1): NP_940954* (*=MANE)

Domains & families (InterPro)

UniProt features (4 total): compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96GI7-F1	67.15	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 102 (showing top): BENPORATH_ES_WITH_H3K27ME3, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, OCT1_03, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, TAATTA_CHX10_01, GAVIN_FOXP3_TARGETS_CLUSTER_P7, NUYTTEN_NIPP1_TARGETS_DN, PYEON_HPV_POSITIVE_TUMORS_DN, MEISSNER_BRAIN_HCP_WITH_H3K27ME3, MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3, MIKKELSEN_NPC_HCP_WITH_H3K27ME3, HOELZEL_NF1_TARGETS_UP, BRUINS_UVC_RESPONSE_LATE, GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

607 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM89A	IFI44L	Q53G44	583
FAM89A	ENGASE	Q8NFI3	484
FAM89A	S100PBP	Q96BU1	479
FAM89A	TRIM67	Q6ZTA4	424
FAM89A	ARHGEF10	O15013	401
FAM89A	ZNF532	Q9HCE3	392
FAM89A	FAM222A	Q5U5X8	364
FAM89A	UPB1	Q9UBR1	357
FAM89A	CATSPERT	Q53TS8	336
FAM89A	PLA2G7	Q13093	335
FAM89A	SDK2	Q58EX2	335
FAM89A	ZFP57	Q9NU63	335
FAM89A	UBE2W	Q96B02	332
FAM89A	KANSL1L	A0AUZ9	322
FAM89A	ANAPC4	Q9UJX5	313

IntAct

8 interactions, top by confidence:

A	B	Type	Score
UBXN2B	VCP	psi-mi:“MI:0914”(association)	0.910
ECE1	FAM89A	psi-mi:“MI:0915”(physical association)	0.370
UBXN2B	PPP1R11	psi-mi:“MI:0914”(association)	0.350
HCN1	POTEF	psi-mi:“MI:0914”(association)	0.350
CDC42	PPP1R12A	psi-mi:“MI:0914”(association)	0.350
CDC42BPB	H2BC18	psi-mi:“MI:0914”(association)	0.350

BioGRID (6): FAM89A (Affinity Capture-MS), FAM89A (Affinity Capture-MS), FAM89A (Affinity Capture-MS), FAM89A (Affinity Capture-MS), FAM89A (Affinity Capture-RNA), FAM89A (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1L168, A1L3T7, A6NGS2, A6QQF7, D4A8G3, O15049, P0C7N2, P0C7N4, P17257, P58660, Q08AY9, Q0V7M8, Q0VDN7, Q14BJ1, Q2NL23, Q3KP66, Q3LUD3, Q3UNU4, Q4LEZ3, Q566R4, Q571B6, Q5BJW5, Q5ND29, Q5RFZ7, Q5XIS1, Q6NSJ2, Q6P1G6, Q6Q0N2, Q7TN12, Q7TSI1, Q811W1, Q8BL43, Q8C7U1, Q8IV03, Q8K1S6, Q8K2P1, Q8N137, Q8N5H3, Q8TE77, Q8WWL2

Diamond homologs: A6QQF7, Q08AY9, Q14BJ1, Q566R4, Q6Q0N2, Q8N5H3, Q96GI7, Q9QUI1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

784 predictions. Top by Δscore:

Variant	Effect	Δscore
1:231039920:CCAT:C	donor_gain	1.0000
1:231020122:CCAAC:C	acceptor_gain	0.9900
1:231020123:CAACC:C	acceptor_gain	0.9900
1:231020126:CC:C	acceptor_loss	0.9900
1:231020140:G:GC	acceptor_gain	0.9900
1:231039916:CTCA:C	donor_loss	0.9900
1:231039917:TCA:T	donor_loss	0.9900
1:231039918:CA:C	donor_loss	0.9900
1:231039919:A:C	donor_loss	0.9900
1:231039920:C:T	donor_loss	0.9900
1:231020123:CAAC:C	acceptor_gain	0.9800
1:231020126:CCT:C	acceptor_gain	0.9800
1:231020128:T:C	acceptor_gain	0.9800
1:231020140:G:C	acceptor_gain	0.9800
1:231039915:ACTC:A	donor_loss	0.9800
1:231039919:A:AC	donor_gain	0.9800
1:231039920:C:CC	donor_gain	0.9800
1:231022670:C:A	donor_gain	0.9600
1:231039919:AC:A	donor_gain	0.9600
1:231039920:CC:C	donor_gain	0.9600
1:231020125:ACCTT:A	acceptor_gain	0.9500
1:231021378:T:A	donor_gain	0.9500
1:231039920:CCA:C	donor_gain	0.9500
1:231020126:CCTTG:C	acceptor_gain	0.9400
1:231020127:C:CC	acceptor_gain	0.9400
1:231020128:T:TC	acceptor_gain	0.9400
1:231039919:ACCAT:A	donor_gain	0.9400
1:231039920:CCATC:C	donor_gain	0.9400
1:231020125:AC:A	acceptor_gain	0.9300
1:231020127:C:T	acceptor_gain	0.9300

AlphaMissense

1163 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:231020107:T:A	D104V	1.000
1:231020069:A:G	S117P	0.999
1:231020077:A:G	L114P	0.999
1:231020086:A:G	L111P	0.999
1:231020098:A:G	L107S	0.999
1:231020107:T:G	D104A	0.999
1:231020117:G:T	R101S	0.999
1:231020119:A:G	L100P	0.999
1:231020119:A:T	L100H	0.999
1:231039921:C:A	M97I	0.999
1:231039921:C:G	M97I	0.999
1:231039921:C:T	M97I	0.999
1:231039922:A:C	M97R	0.999
1:231039934:A:G	L93P	0.999
1:231039934:A:T	L93H	0.999
1:231040033:A:G	I60T	0.999
1:231020098:A:C	L107W	0.998
1:231020102:A:G	S106P	0.998
1:231020106:G:C	D104E	0.998
1:231020106:G:T	D104E	0.998
1:231020107:T:C	D104G	0.998
1:231020108:C:A	D104Y	0.998
1:231020108:C:G	D104H	0.998
1:231020108:C:T	D104N	0.998
1:231020110:A:G	L103P	0.998
1:231039922:A:G	M97T	0.998
1:231039932:G:T	R94S	0.998
1:231020065:A:T	I118N	0.997
1:231020095:A:G	L108P	0.997
1:231020113:T:G	Q102P	0.997

dbSNP variants (sampled 300 via entrez): RS1000167847 (1:231026206 C>T), RS1000278930 (1:231037726 C>T), RS1000323767 (1:231026852 G>A), RS1000364900 (1:231032205 T>C), RS1000551751 (1:231024794 T>C), RS1000712784 (1:231038080 T>A), RS1000857816 (1:231020309 T>A,C), RS1001298454 (1:231020140 G>A), RS1001307099 (1:231041355 C>A), RS1001560469 (1:231033229 T>C), RS1001595617 (1:231040402 C>T), RS1001709671 (1:231027118 C>T), RS1001778474 (1:231027324 G>A), RS1002044463 (1:231038791 T>G), RS1002221082 (1:231023408 G>A)

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
GCST002482_1	Carotid plaque burden (smoking interaction)	7.000000e-06
GCST012048_22	Triglyceride levels	3.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006501	carotid plaque build
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	8
trichostatin A	affects cotreatment, increases expression	3
Cyclosporine	increases expression	3
mercuric bromide	increases expression, affects cotreatment	2
Vorinostat	affects cotreatment, increases expression	2
Panobinostat	increases expression, affects cotreatment	2
Estradiol	increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tetrachlorodibenzodioxin	increases expression	2
Aflatoxin B1	affects expression, increases expression	2
chloroacetaldehyde	increases expression	1
cupric chloride	increases 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, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	increases methylation	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	increases expression	1
Leflunomide	increases expression	1
Cidofovir	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Amiodarone	increases expression	1
Atrazine	increases expression	1
Cisplatin	increases expression	1
Clodronic Acid	increases expression	1
Dietary Carbohydrates	decreases expression	1
Ibuprofen	increases expression	1
Ifosfamide	increases expression	1
Fenofibrate	increases expression	1

Clinical trials (associated diseases)

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