FAM90A1

Summary

FAM90A1 (family with sequence similarity 90 member A1, HGNC:25526) is a protein-coding gene on chromosome 12p13.31, encoding Protein FAM90A1 (Q86YD7).

FAM90A1 belongs to subfamily I of the primate-specific FAM90A gene family, which originated from multiple duplications and rearrangements (Bosch et al., 2007 [PubMed 17684299]).

Source: NCBI Gene 55138 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 116 total
• MANE Select transcript: NM_018088

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25526
Approved symbol	FAM90A1
Name	family with sequence similarity 90 member A1
Location	12p13.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10408
Ensembl gene	ENSG00000171847
Ensembl biotype	protein_coding
OMIM	613041
Entrez	55138

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000307435, ENST00000442295, ENST00000538603, ENST00000890758, ENST00000890759, ENST00000890760, ENST00000890761, ENST00000962992, ENST00000962993, ENST00000962994

RefSeq mRNA: 2 — MANE Select: NM_018088 NM_001319982, NM_018088

CCDS: CCDS31738

Canonical transcript exons

ENST00000538603 — 7 exons

Exon	Start	End
ENSE00001621200	8223449	8223557
ENSE00001663776	8224016	8224215
ENSE00002203707	8227480	8227618
ENSE00002267427	8221260	8222784
ENSE00002283949	8225836	8225992
ENSE00002292485	8224710	8224888
ENSE00002316505	8226272	8226478

Expression profiles

Bgee: expression breadth ubiquitous, 152 present calls, max score 80.00.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.00	gold quality
cortical plate	UBERON:0005343	67.70	gold quality
ventricular zone	UBERON:0003053	67.23	gold quality
right hemisphere of cerebellum	UBERON:0014890	66.97	gold quality
cerebellar hemisphere	UBERON:0002245	65.72	gold quality
cerebellar cortex	UBERON:0002129	65.63	gold quality
cerebellum	UBERON:0002037	63.96	gold quality
nucleus accumbens	UBERON:0001882	63.50	gold quality
right frontal lobe	UBERON:0002810	63.31	gold quality
adenohypophysis	UBERON:0002196	63.14	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	62.84	gold quality
Brodmann (1909) area 9	UBERON:0013540	62.27	gold quality
anterior cingulate cortex	UBERON:0009835	62.24	gold quality
caudate nucleus	UBERON:0001873	62.08	gold quality
pituitary gland	UBERON:0000007	61.69	gold quality
putamen	UBERON:0001874	61.57	gold quality
sperm	CL:0000019	61.21	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	61.18	gold quality
hypothalamus	UBERON:0001898	60.98	gold quality
amygdala	UBERON:0001876	60.77	gold quality
body of pancreas	UBERON:0001150	59.92	gold quality
bone marrow cell	CL:0002092	59.79	gold quality
spinal cord	UBERON:0002240	59.27	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	59.26	gold quality
prefrontal cortex	UBERON:0000451	58.35	gold quality
pancreas	UBERON:0001264	58.27	gold quality
brain	UBERON:0000955	58.11	gold quality
neocortex	UBERON:0001950	57.93	gold quality
left ovary	UBERON:0002119	57.81	gold quality
forebrain	UBERON:0001890	57.72	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting FAM90A1, 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-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-525-5P	99.35	66.85	1615
HSA-MIR-520A-5P	99.35	66.72	1632
HSA-MIR-1228-3P	99.00	66.53	857
HSA-MIR-4272	98.76	68.74	1810
HSA-MIR-6728-3P	98.63	67.63	1534
HSA-MIR-6828-3P	96.06	67.61	1155

Literature-anchored findings (GeneRIF, showing 1)

• Integrated analysis of DNA methylation and mRNA expression profiles to identify key genes involved in the regrowth of clinically non-functioning pituitary adenoma. (PMID:32015217)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam90a1b	ENSMUSG00000043549
mus_musculus	Fam90a1a	ENSMUSG00000079112
rattus_norvegicus	Fam90a1l1	ENSRNOG00000064072

Paralogs (21): FAM90A27P (ENSG00000189348), FAM90A24 (ENSG00000215354), FAM90A5 (ENSG00000215373), FAM90A13 (ENSG00000223885), FAM90A26 (ENSG00000229924), FAM90A15 (ENSG00000230045), FAM90A11 (ENSG00000233115), FAM90A3 (ENSG00000233132), FAM90A20 (ENSG00000233295), FAM90A12 (ENSG00000254229), FAM90A9 (ENSG00000285607), FAM90A16 (ENSG00000285620), FAM90A19 (ENSG00000285657), FAM90A22 (ENSG00000285687), FAM90A17 (ENSG00000285720), FAM90A23 (ENSG00000285765), FAM90A14 (ENSG00000285814), FAM90A18 (ENSG00000285913), FAM90A8 (ENSG00000285937), FAM90A10 (ENSG00000285950), FAM90A7 (ENSG00000285975)

Protein

Protein identifiers

Protein FAM90A1 — Q86YD7 (reviewed: Q86YD7)

All UniProt accessions (2): Q86YD7, F5H7S5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM90 family.

RefSeq proteins (2): NP_001306911, NP_060558* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039213	FAM90	Family
IPR041670	Znf-CCHC_6	Domain

Pfam: PF15288

UniProt features (18 total): sequence variant 6, region of interest 5, compositionally biased region 4, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86YD7-F1	50.50	0.05

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): STAT5A_02, DODD_NASOPHARYNGEAL_CARCINOMA_DN, FIGUEROA_AML_METHYLATION_CLUSTER_5_DN, FOXN3_TARGET_GENES, MIR580_3P, MIR1228_3P, BLANCO_MELO_MERS_COV_INFECTION_MCR5_CELLS_UP, DESCARTES_MAIN_FETAL_SLC26A4_PAEP_POSITIVE_CELLS, HDGF_TARGET_GENES, VAN_DEN_BIGGELAAR_PBMC_PREVNAR_9MO_INFANT_STIMULATED_VS_UNSTIMULATED_8MO_UP, VAN_DEN_BIGGELAAR_PBMC_PREVNAR_9MO_INFANT_STIMULATED_VS_UNSTIMULATED_9MO_UP, GSE2405_0H_VS_3H_A_PHAGOCYTOPHILUM_STIM_NEUTROPHIL_DN, GSE2405_0H_VS_6H_A_PHAGOCYTOPHILUM_STIM_NEUTROPHIL_DN, GSE1566_WT_VS_EZH2_KO_LN_TCELL_UP, GSE22601_DOUBLE_NEGATIVE_VS_DOUBLE_POSITIVE_THYMOCYTE_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

216 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM90A1	ALG1	Q9BT22	767
FAM90A1	CLEC4A	Q9UMR7	518
FAM90A1	C16orf87	Q6PH81	447
FAM90A1	TBC1D26	Q86UD7	407
FAM90A1	USP31	Q70CQ4	399
FAM90A1	ZNF329	Q86UD4	396
FAM90A1	R3HDM2	Q9Y2K5	366
FAM90A1	PGGHG	Q32M88	359
FAM90A1	ZFP41	Q8N8Y5	358
FAM90A1	A0A0G2JH32	A0A0G2JH32	358
FAM90A1	ING2	Q9H160	352
FAM90A1	PNLIPRP3	Q17RR3	348
FAM90A1	ZNF195	O14628	348
FAM90A1	ZNF814	B7Z6K7	336
FAM90A1	HYCC2	Q8IXS8	322

IntAct

559 interactions, top by confidence:

A	B	Type	Score
FAM90A1	GOLGA2	psi-mi:“MI:0915”(physical association)	0.790
GOLGA2	FAM90A1	psi-mi:“MI:0915”(physical association)	0.790
CALCOCO2	FAM90A1	psi-mi:“MI:0915”(physical association)	0.780
FHL3	FAM90A1	psi-mi:“MI:0915”(physical association)	0.780
FAM90A1	ZNF212	psi-mi:“MI:0915”(physical association)	0.780
ZNF212	FAM90A1	psi-mi:“MI:0915”(physical association)	0.780
FAM90A1	CALCOCO2	psi-mi:“MI:0915”(physical association)	0.780
FAM90A1	FHL3	psi-mi:“MI:0915”(physical association)	0.780
FSD2	FAM90A1	psi-mi:“MI:0915”(physical association)	0.720
FAM90A1	CEP55	psi-mi:“MI:0915”(physical association)	0.720
FAM90A1	PSTPIP1	psi-mi:“MI:0915”(physical association)	0.720
FAM90A1	LDOC1	psi-mi:“MI:0915”(physical association)	0.720
TRIM23	FAM90A1	psi-mi:“MI:0915”(physical association)	0.720
TRAF2	FAM90A1	psi-mi:“MI:0915”(physical association)	0.720
KRT31	FAM90A1	psi-mi:“MI:0915”(physical association)	0.720
FAM90A1	KRT40	psi-mi:“MI:0915”(physical association)	0.720
CEP76	FAM90A1	psi-mi:“MI:0915”(physical association)	0.720
FAM90A1	EXOSC8	psi-mi:“MI:0915”(physical association)	0.720
FAM90A1	STAC3	psi-mi:“MI:0915”(physical association)	0.720
FAM90A1	MID2	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (274): FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid), FAM90A1 (Two-hybrid)

ESM2 similar proteins: A0A096LP49, A0A8V8TNH8, A0A8V8TPE2, A6NDY2, A6NIJ5, A6NJQ4, A6NKC0, A6NNH2, A6NNJ1, A8MUA0, A8MWA6, A8MX19, A8MXJ8, A8MXZ1, A8MYA2, B1ASB6, D6RGX4, P0C7V4, P0C7W8, P0C7W9, P0C7X0, P0DV73, P0DV74, P0DV75, P0DV76, Q0VDD7, Q2KIS6, Q3UHD3, Q4R736, Q5SZB4, Q5T8A7, Q5VZ46, Q5XIK6, Q658T7, Q6A025, Q6NTE8, Q6PIX9, Q6ZMY3, Q86Y26, Q86YD7

Diamond homologs: A0A8V8TNH8, A0A8V8TPE2, A6NDY2, A6NIJ5, A6NJQ4, A6NKC0, A6NNH2, A6NNJ1, A8MWA6, A8MX19, A8MXJ8, A8MXZ1, D6RGX4, P0C7V4, P0C7W8, P0C7W9, P0C7X0, P0DV73, P0DV74, P0DV75, P0DV76, Q658T7, Q86YD7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	92
Likely benign	9
Benign	8

Top pathogenic / likely-pathogenic (0)

SpliceAI

814 predictions. Top by Δscore:

Variant	Effect	Δscore
12:8222780:GCAAC:G	acceptor_gain	1.0000
12:8222781:CAAC:C	acceptor_gain	1.0000
12:8222781:CAACC:C	acceptor_gain	1.0000
12:8222782:AAC:A	acceptor_gain	1.0000
12:8222785:C:CC	acceptor_gain	1.0000
12:8222786:T:C	acceptor_loss	1.0000
12:8223447:AC:A	donor_gain	1.0000
12:8223448:CC:C	donor_gain	1.0000
12:8223448:CCCT:C	donor_gain	1.0000
12:8224042:AT:A	donor_gain	1.0000
12:8224211:TTGAG:T	acceptor_gain	1.0000
12:8224706:TTA:T	donor_loss	1.0000
12:8224708:A:AC	donor_gain	1.0000
12:8224708:AC:A	donor_gain	1.0000
12:8224708:ACC:A	donor_gain	1.0000
12:8224708:ACCC:A	donor_loss	1.0000
12:8224709:C:A	donor_loss	1.0000
12:8224709:C:CA	donor_gain	1.0000
12:8224709:CC:C	donor_gain	1.0000
12:8224709:CCC:C	donor_gain	1.0000
12:8224709:CCCT:C	donor_gain	1.0000
12:8224709:CCCTG:C	donor_gain	1.0000
12:8224884:GTCAC:G	acceptor_gain	1.0000
12:8224885:TCAC:T	acceptor_gain	1.0000
12:8224886:CAC:C	acceptor_gain	1.0000
12:8224886:CACC:C	acceptor_gain	1.0000
12:8224887:AC:A	acceptor_gain	1.0000
12:8224888:CC:C	acceptor_gain	1.0000
12:8224888:CCTGA:C	acceptor_loss	1.0000
12:8224889:C:CA	acceptor_loss	1.0000

AlphaMissense

2996 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:8222029:A:C	F396L	0.920
12:8222029:A:T	F396L	0.920
12:8222031:A:G	F396L	0.920
12:8224189:A:C	F50L	0.906
12:8224189:A:T	F50L	0.906
12:8224191:A:G	F50L	0.906
12:8222007:A:G	W404R	0.881
12:8222007:A:T	W404R	0.881
12:8222005:C:A	W404C	0.848
12:8222005:C:G	W404C	0.848
12:8224164:A:G	C59R	0.841
12:8222299:C:A	K306N	0.821
12:8222299:C:G	K306N	0.821
12:8224171:A:C	S56R	0.821
12:8224171:A:T	S56R	0.821
12:8224173:T:G	S56R	0.821
12:8224163:C:G	C59S	0.818
12:8224164:A:T	C59S	0.818
12:8222359:G:C	F286L	0.797
12:8222359:G:T	F286L	0.797
12:8222361:A:G	F286L	0.797
12:8224183:G:C	H52Q	0.793
12:8224183:G:T	H52Q	0.793
12:8222030:A:G	F396S	0.788
12:8222278:G:C	F313L	0.754
12:8222278:G:T	F313L	0.754
12:8222280:A:G	F313L	0.754
12:8224187:C:T	G51D	0.740
12:8224208:C:G	C44S	0.739
12:8224209:A:T	C44S	0.739

dbSNP variants (sampled 300 via entrez): RS1000549683 (12:8224086 A>G), RS1002502413 (12:8228146 T>C), RS1002784176 (12:8227800 G>A,T), RS1003511059 (12:8226576 G>A), RS1003794091 (12:8226249 A>T), RS1004071826 (12:8220902 C>A,T), RS1004115005 (12:8225499 A>G), RS1004466749 (12:8225116 G>A,T), RS1005066092 (12:8223703 G>A,T), RS1005529620 (12:8223962 A>C), RS1005748467 (12:8226587 C>T), RS1006215320 (12:8226878 T>C), RS1006591476 (12:8227377 G>A,C), RS1007538130 (12:8221520 CG>C,CGG), RS1007544311 (12:8225527 G>A)

Disease associations

OMIM: gene MIM:613041 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST003854_37	Gut microbiota (functional units)	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007874	gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	increases expression	2
aristolochic acid I	increases expression	1
propionaldehyde	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
versicolorin A	increases expression	1
pentanal	increases expression	1
licochalcone B	increases expression	1
(+)-JQ1 compound	decreases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Endosulfan	decreases expression	1
Melphalan	decreases expression	1
Plant Oils	increases expression	1
Silicon Dioxide	increases expression	1
Valproic Acid	increases methylation	1
Lithium Chloride	decreases expression	1

Clinical trials (associated diseases)

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