FAM228A

Summary

FAM228A (family with sequence similarity 228 member A, HGNC:34418) is a protein-coding gene on chromosome 2p23.3, encoding Protein FAM228A (Q86W67).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 30 total
• MANE Select transcript: NM_001040710

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34418
Approved symbol	FAM228A
Name	family with sequence similarity 228 member A
Location	2p23.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ30851
Ensembl gene	ENSG00000186453
Ensembl biotype	protein_coding
Entrez	653140

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 nonsense_mediated_decay

ENST00000295150, ENST00000415196, ENST00000432434, ENST00000456591, ENST00000965618

RefSeq mRNA: 1 — MANE Select: NM_001040710 NM_001040710

CCDS: CCDS42659

Canonical transcript exons

ENST00000295150 — 6 exons

Exon	Start	End
ENSE00001334872	24175053	24175174
ENSE00001346865	24190412	24191698
ENSE00003460257	24183285	24183372
ENSE00003495154	24177802	24177870
ENSE00003506185	24183495	24183645
ENSE00003651002	24175467	24175573

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 95.83.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4173 / max 100.5920, expressed in 140 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
19177	0.3063	108
19176	0.1109	59

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	95.83	gold quality
left testis	UBERON:0004533	92.48	gold quality
right testis	UBERON:0004534	92.21	gold quality
testis	UBERON:0000473	92.09	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.01	gold quality
quadriceps femoris	UBERON:0001377	80.34	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.17	gold quality
thymus	UBERON:0002370	75.36	silver quality
mucosa of stomach	UBERON:0001199	71.02	gold quality
descending thoracic aorta	UBERON:0002345	69.80	gold quality
prefrontal cortex	UBERON:0000451	69.34	gold quality
apex of heart	UBERON:0002098	68.45	gold quality
cortical plate	UBERON:0005343	68.29	gold quality
frontal cortex	UBERON:0001870	68.26	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	67.77	gold quality
anterior cingulate cortex	UBERON:0009835	67.23	gold quality
omental fat pad	UBERON:0010414	67.21	gold quality
cerebral cortex	UBERON:0000956	67.16	gold quality
thoracic aorta	UBERON:0001515	67.02	gold quality
adipose tissue	UBERON:0001013	66.93	gold quality
ascending aorta	UBERON:0001496	66.82	gold quality
right frontal lobe	UBERON:0002810	66.82	gold quality
subcutaneous adipose tissue	UBERON:0002190	66.69	gold quality
superior frontal gyrus	UBERON:0002661	66.58	gold quality
Brodmann (1909) area 9	UBERON:0013540	66.19	gold quality
left coronary artery	UBERON:0001626	66.14	gold quality
corpus callosum	UBERON:0002336	66.14	gold quality
amygdala	UBERON:0001876	65.79	gold quality
right atrium auricular region	UBERON:0006631	65.70	gold quality
temporal lobe	UBERON:0001871	65.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.90

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting FAM228A, 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-6867-5P	100.00	82.21	3464
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-12117	99.50	67.57	868
HSA-MIR-513A-3P	99.39	70.63	3620
HSA-MIR-513C-3P	99.39	70.63	3620
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-3199	99.17	65.19	696
HSA-MIR-3688-5P	99.12	69.67	1091
HSA-MIR-3606-3P	99.11	69.84	3254
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-140-3P	99.04	67.69	1324
HSA-MIR-155-3P	99.03	67.99	924
HSA-MIR-935	98.82	69.36	1072
HSA-MIR-7113-3P	98.75	65.71	1120

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam228a	ENSDARG00000042936
mus_musculus	Fam228a	ENSMUSG00000079177
rattus_norvegicus	Fam228a	ENSRNOG00000050114

Paralogs (1): FAM228B (ENSG00000219626)

Protein

Protein identifiers

Protein FAM228A — Q86W67 (reviewed: Q86W67)

All UniProt accessions (4): F2Z3J0, H7C3M9, Q86W67, H7C4B8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM228 family.

RefSeq proteins (1): NP_001035800* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040046	FAM228	Family

UniProt features (2 total): chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86W67-F1	63.60	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 20 (showing top): CATTTCA_MIR203, BRUINS_UVC_RESPONSE_EARLY_LATE, GLI1_TARGET_GENES, MIR6867_5P, MIR493_5P, MIR3685, MIR4802_3P, GSE10273_HIGH_IL7_VS_HIGH_IL7_AND_IRF4_IN_IRF4_8_NULL_PRE_BCELL_DN, MIR12117, MIR4330, chr2p23, DESCARTES_FETAL_PLACENTA_SMOOTH_MUSCLE_CELLS, DNMT3A_TARGET_GENES, GSE29615_DAY3_VS_DAY7_LAIV_FLU_VACCINE_PBMC_UP, GSE1112_OT1_CD8AB_VS_HY_CD8AA_THYMOCYTE_RTOC_CULTURE_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

164 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM228A	SPIN3	Q5JUX0	447
FAM228A	TMEM71	Q6P5X7	435
FAM228A	ZGRF1	Q86YA3	431
FAM228A	RFX8	Q6ZV50	430
FAM228A	CCDC32	Q9BV29	419
FAM228A	GDPD4	Q6W3E5	418
FAM228A	SLC25A47	Q6Q0C1	417
FAM228A	FAM174B	Q3ZCQ3	400
FAM228A	ZNF101	Q8IZC7	400
FAM228A	SPATA17	Q96L03	397
FAM228A	GSC	P56915	370
FAM228A	PPP1R3G	B7ZBB8	370
FAM228A	VSTM1	Q6UX27	370
FAM228A	ADAM21	Q9UKJ8	370
FAM228A	TOR3A	Q9H497	369

IntAct

57 interactions, top by confidence:

A	B	Type	Score
FAM228A	IFNA21	psi-mi:“MI:0915”(physical association)	0.590
CDKN2D	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
PLEKHA7	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
SPANXN3	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
GYS1	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
LMO4	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
MLH1	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
HSF2BP	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
FAM228A	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
FAM228A	FAM90A1	psi-mi:“MI:0915”(physical association)	0.560
ZNF76	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
LMO2	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
FAM228A	ENKD1	psi-mi:“MI:0915”(physical association)	0.560
FAM228A	EAF1	psi-mi:“MI:0915”(physical association)	0.560
BYSL	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
SAT1	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
TNS2	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
COX5B	FAM228A	psi-mi:“MI:0915”(physical association)	0.560
GYS1	FAM228A	psi-mi:“MI:0915”(physical association)	0.000
LMO4	FAM228A	psi-mi:“MI:0915”(physical association)	0.000
MLH1	FAM228A	psi-mi:“MI:0915”(physical association)	0.000
HSF2BP	FAM228A	psi-mi:“MI:0915”(physical association)	0.000
SCNM1	FAM228A	psi-mi:“MI:0915”(physical association)	0.000
FAM90A1	FAM228A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (22): IFNA21 (Affinity Capture-MS), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid), FAM228A (Two-hybrid)

ESM2 similar proteins: A0A1B0GUC4, A1STV0, A6NGY3, B8NI18, O54842, O84275, O89085, P03238, P03331, P05911, P11888, P26548, P26549, P27224, P56555, P87318, Q08270, Q08588, Q0P641, Q1KN10, Q1KN12, Q1KN16, Q1KN19, Q1KN23, Q1X6X9, Q1X6Y0, Q1X6Y1, Q1X6Y7, Q1X6Z0, Q1X6Z2, Q1X6Z3, Q1X700, Q1X711, Q2YDL7, Q5BL73, Q5RDL5, Q6AY31, Q6W0C5, Q84295, Q86W67

Diamond homologs: A6QQ68, P0C875, Q32KQ1, Q497Q6, Q5XIN5, Q86W67, Q8CDW1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

957 predictions. Top by Δscore:

Variant	Effect	Δscore
2:24175532:T:G	donor_gain	1.0000
2:24183362:GT:G	donor_gain	1.0000
2:24183641:TACAG:T	donor_loss	1.0000
2:24183642:ACAG:A	donor_loss	1.0000
2:24183642:ACAGG:A	donor_loss	1.0000
2:24183643:CAG:C	donor_loss	1.0000
2:24183644:AGG:A	donor_loss	1.0000
2:24183644:AGGTA:A	donor_loss	1.0000
2:24183645:GG:G	donor_loss	1.0000
2:24183646:G:GA	donor_loss	1.0000
2:24183647:T:G	donor_loss	1.0000
2:24183652:A:G	donor_gain	1.0000
2:24190410:A:AG	acceptor_gain	1.0000
2:24190411:G:GG	acceptor_gain	1.0000
2:24175462:CTCA:C	acceptor_loss	0.9900
2:24175463:TCA:T	acceptor_loss	0.9900
2:24175464:CAGGG:C	acceptor_loss	0.9900
2:24175465:A:AC	acceptor_loss	0.9900
2:24175465:A:AG	acceptor_gain	0.9900
2:24175465:AG:A	acceptor_gain	0.9900
2:24175465:AGG:A	acceptor_gain	0.9900
2:24175466:G:GG	acceptor_gain	0.9900
2:24175466:GG:G	acceptor_gain	0.9900
2:24175466:GGG:G	acceptor_gain	0.9900
2:24175570:GGAG:G	donor_gain	0.9900
2:24175571:G:GT	donor_gain	0.9900
2:24175572:AGGT:A	donor_loss	0.9900
2:24175573:GGT:G	donor_loss	0.9900
2:24177796:TTTTA:T	acceptor_loss	0.9900
2:24177797:TTTAG:T	acceptor_loss	0.9900

AlphaMissense

1355 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:24190500:T:C	F164L	0.910
2:24190502:C:A	F164L	0.910
2:24190502:C:G	F164L	0.910
2:24175517:T:C	F13L	0.903
2:24175519:C:A	F13L	0.903
2:24175519:C:G	F13L	0.903
2:24177842:T:A	I45K	0.882
2:24190488:T:C	F160L	0.882
2:24190490:T:A	F160L	0.882
2:24190490:T:G	F160L	0.882
2:24175541:T:A	W21R	0.876
2:24175541:T:C	W21R	0.876
2:24175570:G:A	M30I	0.856
2:24175570:G:C	M30I	0.856
2:24175570:G:T	M30I	0.856
2:24177842:T:C	I45T	0.853
2:24177829:G:C	A41P	0.836
2:24177809:C:A	A34D	0.816
2:24177842:T:G	I45R	0.814
2:24183300:T:C	F60L	0.801
2:24183302:T:A	F60L	0.801
2:24183302:T:G	F60L	0.801
2:24177847:T:C	F47L	0.795
2:24177849:T:A	F47L	0.795
2:24177849:T:G	F47L	0.795
2:24175543:G:C	W21C	0.788
2:24175543:G:T	W21C	0.788
2:24177806:T:C	L33S	0.778
2:24177808:G:C	A34P	0.774
2:24183569:T:C	F109L	0.773

dbSNP variants (sampled 300 via entrez): RS1000857158 (2:24177568 G>A,T), RS1000882387 (2:24184441 T>C,G), RS1000913495 (2:24184228 A>G), RS1000915235 (2:24189847 C>G,T), RS1000971770 (2:24190007 C>G), RS1001101852 (2:24190084 C>T), RS1001400115 (2:24177457 A>G), RS1001469808 (2:24190340 C>A,G), RS1001885712 (2:24183184 T>A,C), RS1001919842 (2:24182899 C>T), RS1002070848 (2:24189202 C>T), RS1002140389 (2:24187697 G>A), RS1002372239 (2:24189465 T>A), RS1002484761 (2:24176111 A>C,G), RS1002656138 (2:24179593 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
GCST005212_4	Asthma	2.000000e-07
GCST90002407_215	White blood cell count	2.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation	1
ethyl-p-hydroxybenzoate	decreases expression	1
bisphenol S	decreases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Drugs, Chinese Herbal	increases expression	1
Naphthoquinones	increases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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