FAM229A

Summary

FAM229A (family with sequence similarity 229 member A, HGNC:44652) is a protein-coding gene on chromosome 1p35.1, encoding Protein FAM229A (H3BQW9). It is a selective cancer dependency (DepMap: 14.6% of cell lines).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 30 total
• Cancer dependency (DepMap): dependent in 14.6% of screened cell lines
• MANE Select transcript: NM_001167676

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44652
Approved symbol	FAM229A
Name	family with sequence similarity 229 member A
Location	1p35.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000225828
Ensembl biotype	protein_coding
Entrez	100128071

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000415596, ENST00000416512, ENST00000428500, ENST00000432622

RefSeq mRNA: 1 — MANE Select: NM_001167676 NM_001167676

CCDS: CCDS57985

Canonical transcript exons

ENST00000432622 — 3 exons

Exon	Start	End
ENSE00001656147	32361958	32362485
ENSE00001683224	32361270	32361535
ENSE00001694118	32361730	32361876

Expression profiles

Bgee: expression breadth ubiquitous, 159 present calls, max score 97.21.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3132 / max 129.4614, expressed in 94 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11542	0.1568	65
11540	0.1117	12
11539	0.0240	5
11541	0.0207	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	97.21	gold quality
left testis	UBERON:0004533	97.00	gold quality
testis	UBERON:0000473	92.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.30	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.31	gold quality
cerebellar hemisphere	UBERON:0002245	86.96	gold quality
cerebellar cortex	UBERON:0002129	86.74	gold quality
right lobe of liver	UBERON:0001114	85.58	gold quality
granulocyte	CL:0000094	85.23	gold quality
lower esophagus mucosa	UBERON:0035834	84.79	gold quality
right ovary	UBERON:0002118	84.73	gold quality
left ovary	UBERON:0002119	84.61	gold quality
left uterine tube	UBERON:0001303	84.17	gold quality
mucosa of stomach	UBERON:0001199	83.81	gold quality
cerebellum	UBERON:0002037	83.76	gold quality
mucosa of transverse colon	UBERON:0004991	83.73	gold quality
endocervix	UBERON:0000458	83.72	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.67	gold quality
spleen	UBERON:0002106	83.50	gold quality
small intestine Peyer’s patch	UBERON:0003454	83.10	gold quality
metanephros cortex	UBERON:0010533	82.86	gold quality
left adrenal gland cortex	UBERON:0035825	82.54	gold quality
skin of leg	UBERON:0001511	82.20	gold quality
right uterine tube	UBERON:0001302	82.14	gold quality
right lung	UBERON:0002167	82.12	gold quality
left adrenal gland	UBERON:0001234	81.82	gold quality
body of uterus	UBERON:0009853	81.54	gold quality
skin of abdomen	UBERON:0001416	81.50	gold quality
right adrenal gland	UBERON:0001233	81.24	gold quality
left lobe of thyroid gland	UBERON:0001120	81.21	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting FAM229A, 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-3662	99.99	73.82	5684
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-6737-3P	98.95	68.56	1577
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-4711-5P	98.89	68.00	965
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-5008-3P	98.73	67.50	1433
HSA-MIR-6818-3P	98.56	68.23	1307
HSA-MIR-4773	98.35	67.30	1710
HSA-MIR-4289	98.26	66.90	810
HSA-MIR-7112-3P	97.67	68.77	948
HSA-MIR-1469	65.89	55.19	6

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 14.6% of screened cell lines.

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam229a	ENSMUSG00000078554
rattus_norvegicus	Fam229a	ENSRNOG00000042787

Paralogs (1): FAM229B (ENSG00000203778)

Protein

Protein identifiers

Protein FAM229A — H3BQW9 (reviewed: H3BQW9)

All UniProt accessions (2): H3BQW9, H3BMD6

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM229 family.

RefSeq proteins (1): NP_001161148* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028025	FAM229	Family

Pfam: PF14982

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-H3BQW9-F1	63.38	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 23 (showing top): chr1p35, HMGA1_TARGET_GENES, MIR4773, MIR7157_3P, MIR6737_3P, MIR5008_3P, GSE11924_TH1_VS_TH2_CD4_TCELL_DN, GAO_STOMACH_24W_C1_PROCRPOS_MULTIPOTENT_PROGENITOR, DESCARTES_FETAL_KIDNEY_ERYTHROBLASTS, GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_2H_UP, HE_LIM_SUN_FETAL_LUNG_C1_SMG_CELL, GSE27786_CD8_TCELL_VS_NKTCELL_DN, BERGER_PLATELET_HYPERREACTIVITY_PRESS_UP, GSE32423_MEMORY_VS_NAIVE_CD8_TCELL_IL7_IL4_UP, GSE9988_LPS_VS_LOW_LPS_MONOCYTE_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

96 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM229A	C19orf73	Q9NVV2	664
FAM229A	C1QTNF9B	B2RNN3	582
FAM229A	SETSIP	P0DME0	544
FAM229A	LY6G5C	Q5SRR4	453
FAM229A	CDC42EP5	Q6NZY7	445
FAM229A	TAS2R14	Q9NYV8	433
FAM229A	POLR3G	O15318	406
FAM229A	SLITRK6	Q9H5Y7	370
FAM229A	KRT23	Q9C075	353
FAM229A	PLA2G15	Q8NCC3	349
FAM229A	NNAT	Q16517	323
FAM229A	MXRA5	Q9NR99	322
FAM229A	TARS2	Q9BW92	314
FAM229A	CRADD	P78560	305
FAM229A	ATP6V0D2	Q8N8Y2	302
FAM229A	ACOX2	Q99424	302

IntAct

0 interactions, top by confidence:

BioGRID (1): FAM229A (Affinity Capture-RNA)

ESM2 similar proteins: A0A1B0GUT2, A0A3Q1LFG5, A1L4Q6, A2RUQ5, A8MQB3, A8MU10, B1ANY3, C0HM98, H3BQW9, J3KSC0, P0C092, P0DMU3, P0DPA3, P24026, P59020, P59021, P59052, P87743, Q06250, Q0IIN9, Q0VFX4, Q14695, Q4R3X9, Q4VX62, Q52M75, Q5SR53, Q6ZUF6, Q6ZWC4, Q71F78, Q7Z4H9, Q8JMY5, Q8JMZ5, Q8JN06, Q8N2C9, Q8N2X6, Q8N3U1, Q8N9X3, Q8NAA6, Q8NBC4, Q8NDY4

Diamond homologs: A5LFY3, B0BND4, B2KGE5, H3BQW9, Q0D252, Q4G0N7, Q8CF36

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	28
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

435 predictions. Top by Δscore:

Variant	Effect	Δscore
1:32362417:GGC:G	donor_gain	1.0000
1:32361725:CTTA:C	donor_loss	0.9900
1:32361726:TTACC:T	donor_loss	0.9900
1:32361727:TACC:T	donor_loss	0.9900
1:32361728:A:T	donor_loss	0.9900
1:32361729:C:CA	donor_loss	0.9900
1:32362418:GC:G	donor_gain	0.9900
1:32362419:C:G	donor_gain	0.9900
1:32363585:A:AG	acceptor_gain	0.9900
1:32363591:TCAG:T	acceptor_gain	0.9900
1:32363593:A:AC	acceptor_loss	0.9900
1:32363593:A:AG	acceptor_gain	0.9900
1:32363594:G:GG	acceptor_gain	0.9900
1:32363594:G:T	acceptor_loss	0.9900
1:32363594:GA:G	acceptor_gain	0.9900
1:32363594:GAGT:G	acceptor_gain	0.9900
1:32361729:CCTGA:C	donor_gain	0.9800
1:32361731:TG:T	donor_gain	0.9800
1:32362416:GGGC:G	donor_gain	0.9800
1:32362430:G:GA	donor_gain	0.9800
1:32362433:G:GA	donor_gain	0.9800
1:32362435:T:TA	donor_gain	0.9800
1:32362436:A:AA	donor_gain	0.9800
1:32363591:TCAGA:T	acceptor_gain	0.9800
1:32363592:CAG:C	acceptor_gain	0.9800
1:32363592:CAGAG:C	acceptor_gain	0.9800
1:32363593:AGA:A	acceptor_gain	0.9800
1:32363594:GAG:G	acceptor_gain	0.9800
1:32363594:GAGTT:G	acceptor_gain	0.9800
1:32361728:A:AC	donor_gain	0.9700

AlphaMissense

793 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:32361482:A:T	I112N	0.989
1:32361476:A:T	V114D	0.987
1:32361522:A:G	C99R	0.985
1:32361474:A:C	Y115D	0.982
1:32361823:A:G	F63S	0.980
1:32361482:A:C	I112S	0.979
1:32361525:G:T	R98S	0.975
1:32361505:G:C	C104W	0.972
1:32361521:C:G	C99S	0.972
1:32361522:A:T	C99S	0.972
1:32361530:A:T	L96H	0.972
1:32361520:G:C	C99W	0.971
1:32361521:C:T	C99Y	0.970
1:32361508:G:C	H103Q	0.969
1:32361508:G:T	H103Q	0.969
1:32361479:T:A	D113V	0.968
1:32361823:A:C	F63C	0.968
1:32361474:A:T	Y115N	0.967
1:32361817:A:T	I65N	0.966
1:32361822:G:C	F63L	0.963
1:32361822:G:T	F63L	0.963
1:32361824:A:G	F63L	0.963
1:32361500:G:T	T106K	0.958
1:32361506:C:T	C104Y	0.956
1:32361510:G:C	H103D	0.956
1:32361497:A:G	L107P	0.955
1:32361503:A:T	L105Q	0.954
1:32361503:A:G	L105P	0.953
1:32361482:A:G	I112T	0.951
1:32361805:T:A	D69V	0.950

dbSNP variants (sampled 300 via entrez): RS1000068694 (1:32362322 A>G), RS1000652777 (1:32361200 G>A), RS1000982482 (1:32360986 C>T), RS1002459355 (1:32361849 G>A), RS1002472014 (1:32360794 A>G), RS1003416754 (1:32364449 CCTT>C), RS1003728868 (1:32363037 C>A,G,T), RS1004007596 (1:32364338 T>C), RS1004800162 (1:32361860 C>T), RS1004872163 (1:32362080 G>A,C), RS1005879120 (1:32363011 G>A,T), RS1006441808 (1:32361803 A>C), RS1006569479 (1:32362698 C>A,T), RS1006654552 (1:32361621 C>A,T), RS1007444061 (1:32363668 G>A,C,T)

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

1 associations (top):

Study	Trait	p-value
GCST008758_22	Pre-treatment viral load in HIV-1 infection	4.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010125	viral load

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
sodium arsenite	decreases expression	1
clothianidin	decreases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	decreases expression	1
Leflunomide	decreases expression	1
Cisplatin	decreases expression	1
Estradiol	decreases expression	1
Thiram	increases expression	1
Valproic Acid	increases methylation, decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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