FAM90A9

Summary

FAM90A9 (family with sequence similarity 90 member A9, HGNC:32257) is a protein-coding gene on chromosome 8p23.1, encoding Protein FAM90A9 (A6NNJ1).

FAM90A9 belongs to subfamily II of the primate-specific FAM90A gene family, which originated from multiple duplications and rearrangements (Bosch et al., 2007 [PubMed 17684299]). For background information on the FAM90A gene family, as well as information on the evolution of FAM90A genes, see FAM90A1 (MIM 613041).

Source: NCBI Gene 441327 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001164448

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32257
Approved symbol	FAM90A9
Name	family with sequence similarity 90 member A9
Location	8p23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000285607
Ensembl biotype	protein_coding
OMIM	613046
Entrez	441327

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000648344

RefSeq mRNA: 4 — MANE Select: NM_001164448 NM_001164448, NM_001421777, NM_001421779, NM_001421789

Canonical transcript exons

ENST00000648344 — 4 exons

Exon	Start	End
ENSE00002146060	7761947	7762146
ENSE00002184450	7762605	7762713
ENSE00002192447	7761330	7761452
ENSE00003832332	7763378	7764340

Expression profiles

Bgee: expression breadth broad, 15 present calls, max score 44.64.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	44.64	gold quality
colonic epithelium	UBERON:0000397	42.33	gold quality
cortical plate	UBERON:0005343	39.82	gold quality
ganglionic eminence	UBERON:0004023	38.86	gold quality
mucosa of stomach	UBERON:0001199	37.34	silver quality
bone marrow cell	CL:0002092	36.16	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
endocervix	UBERON:0000458	33.19	gold quality
duodenum	UBERON:0002114	32.33	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
uterine cervix	UBERON:0000002	30.53	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.52	gold quality
liver	UBERON:0002107	28.87	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	28.72	gold quality
gall bladder	UBERON:0002110	28.36	gold quality
urinary bladder	UBERON:0001255	27.73	gold quality
lymph node	UBERON:0000029	27.57	gold quality
islet of Langerhans	UBERON:0000006	27.54	gold quality
tonsil	UBERON:0002372	27.05	gold quality
ectocervix	UBERON:0012249	26.79	silver quality
leukocyte	CL:0000738	26.67	gold quality
monocyte	CL:0000576	26.58	gold quality
blood	UBERON:0000178	26.54	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
placenta	UBERON:0001987	25.81	gold quality
muscle of leg	UBERON:0001383	25.46	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.15

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

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

Paralogs (21): FAM90A1 (ENSG00000171847), FAM90A27P (ENSG00000189348), FAM90A24 (ENSG00000215354), FAM90A5 (ENSG00000215373), FAM90A13 (ENSG00000223885), FAM90A26 (ENSG00000229924), FAM90A15 (ENSG00000230045), FAM90A11 (ENSG00000233115), FAM90A3 (ENSG00000233132), FAM90A20 (ENSG00000233295), FAM90A12 (ENSG00000254229), FAM90A16 (ENSG00000285620), FAM90A19 (ENSG00000285657), FAM90A22 (ENSG00000285687), FAM90A17 (ENSG00000285720), FAM90A23 (ENSG00000285765), FAM90A14 (ENSG00000285814), FAM90A18 (ENSG00000285913), FAM90A8 (ENSG00000285937), FAM90A10 (ENSG00000285950), FAM90A7 (ENSG00000285975)

Protein

Protein identifiers

Protein FAM90A9 — A6NNJ1 (reviewed: A6NNJ1)

All UniProt accessions (1): A6NNJ1

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM90 family.

RefSeq proteins (4): NP_001157920, NP_001408706, NP_001408708, NP_001408718 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039213	FAM90	Family
IPR041670	Znf-CCHC_6	Domain

Pfam: PF15288

UniProt features (7 total): region of interest 3, compositionally biased region 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NNJ1-F1	50.05	0.04

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): FORTSCHEGGER_PHF8_TARGETS_UP, chr8p23

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A096LP49, A0A8V8TNH8, A0A8V8TPE2, A2VE02, A5D7I0, A6NDY2, A6NGG8, A6NIJ5, A6NNJ1, A8MXJ8, A8MYA2, B1ASB6, B2RW88, D6RGX4, O60269, P0C7V4, P0C7W8, P0C7W9, P0C7X0, P0DV75, P0DV76, Q2KIS6, Q2NL68, Q3SY00, Q4R736, Q4V8B5, Q5RCQ2, Q5SZB4, Q5VZ46, Q5XIK6, Q658T7, Q66JV7, Q6NS69, Q6PAC4, Q6ZMY3, Q76N32, Q7TSA6, Q7Z591, Q80VW7, Q80X53

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

2999 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:7761971:T:C	F50L	0.978
8:7761973:T:A	F50L	0.978
8:7761973:T:G	F50L	0.978
8:7761998:T:C	C59R	0.974
8:7761953:T:A	C44S	0.968
8:7761954:G:C	C44S	0.968
8:7761979:C:A	H52Q	0.967
8:7761979:C:G	H52Q	0.967
8:7761962:T:A	C47S	0.964
8:7761963:G:C	C47S	0.964
8:7761998:T:A	C59S	0.962
8:7761999:G:C	C59S	0.962
8:7761963:G:A	C47Y	0.956
8:7761952:G:C	K43N	0.955
8:7761952:G:T	K43N	0.955
8:7761975:G:A	G51D	0.953
8:7761989:A:C	S56R	0.951
8:7761991:T:A	S56R	0.951
8:7761991:T:G	S56R	0.951
8:7761953:T:C	C44R	0.948
8:7764131:T:C	F396L	0.948
8:7764133:C:A	F396L	0.948
8:7764133:C:G	F396L	0.948
8:7764155:T:A	W404R	0.945
8:7764155:T:C	W404R	0.945
8:7761962:T:C	C47R	0.943
8:7761963:G:T	C47F	0.940
8:7761964:C:G	C47W	0.929
8:7762000:C:G	C59W	0.923
8:7761955:C:G	C44W	0.920

dbSNP variants (sampled 300 via entrez): RS1042368125 (8:7764667 G>A,C), RS111448288 (8:7764686 C>A,G,T), RS111745191 (8:7761592 G>A), RS111793240 (8:7763639 A>C,G), RS112155279 (8:7761511 G>C), RS112512847 (8:7761758 C>A), RS113799453 (8:7760575 A>C), RS1157809412 (8:7764659 A>G,T), RS1160972521 (8:7764632 T>G), RS1161881669 (8:7764449 C>T), RS1164724661 (8:7763959 C>A,T), RS1166179622 (8:7764831 G>A), RS1167656908 (8:7763667 C>A,T), RS1169962304 (8:7763977 G>T), RS1170442609 (8:7764084 A>G)

Disease associations

OMIM: gene MIM:613046 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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