FAM209B

Summary

FAM209B (family with sequence similarity 209 member B, HGNC:16101) is a protein-coding gene on chromosome 20q13.31, encoding Protein FAM209B (Q5JX69). May play a role in sperm acrosome biogenesis.

Predicted to be involved in acrosome assembly. Located in acrosomal vesicle.

Source: NCBI Gene 388799 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 12 total
• MANE Select transcript: NM_001013646

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16101
Approved symbol	FAM209B
Name	family with sequence similarity 209 member B
Location	20q13.31
Locus type	gene with protein product
Status	Approved
Aliases	dJ1153D9.4
Ensembl gene	ENSG00000213714
Ensembl biotype	protein_coding
Entrez	388799

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000371325

RefSeq mRNA: 1 — MANE Select: NM_001013646 NM_001013646

CCDS: CCDS33494

Canonical transcript exons

ENST00000371325 — 2 exons

Exon	Start	End
ENSE00000845716	56536172	56536520
ENSE00001768052	56533246	56533590

Expression profiles

Bgee: expression breadth ubiquitous, 159 present calls, max score 96.76.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	96.76	gold quality
left testis	UBERON:0004533	96.68	gold quality
right testis	UBERON:0004534	96.20	gold quality
testis	UBERON:0000473	93.55	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.50	gold quality
adult organism	UBERON:0007023	90.85	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.74	gold quality
blood	UBERON:0000178	73.49	gold quality
granulocyte	CL:0000094	71.12	gold quality
tibialis anterior	UBERON:0001385	67.70	silver quality
spleen	UBERON:0002106	67.23	gold quality
leukocyte	CL:0000738	67.03	gold quality
monocyte	CL:0000576	66.82	gold quality
apex of heart	UBERON:0002098	64.78	gold quality
skin of leg	UBERON:0001511	63.85	gold quality
gastrocnemius	UBERON:0001388	62.45	gold quality
ileal mucosa	UBERON:0000331	62.17	silver quality
muscle of leg	UBERON:0001383	61.47	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	61.24	gold quality
endothelial cell	CL:0000115	61.20	gold quality
skin of abdomen	UBERON:0001416	61.05	gold quality
lower esophagus mucosa	UBERON:0035834	60.97	gold quality
zone of skin	UBERON:0000014	60.05	gold quality
pancreatic ductal cell	CL:0002079	60.00	silver quality
mucosa of stomach	UBERON:0001199	59.96	gold quality
buccal mucosa cell	CL:0002336	59.63	gold quality
nasal cavity mucosa	UBERON:0001826	59.41	gold quality
upper lobe of left lung	UBERON:0008952	59.34	gold quality
lymph node	UBERON:0000029	59.23	gold quality
small intestine Peyer’s patch	UBERON:0003454	58.95	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.06

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam209	ENSMUSG00000027505
rattus_norvegicus	Fam209	ENSRNOG00000005235

Paralogs (1): FAM209A (ENSG00000124103)

Protein

Protein identifiers

Protein FAM209B — Q5JX69 (reviewed: Q5JX69)

All UniProt accessions (1): Q5JX69

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in sperm acrosome biogenesis.

Subcellular location. Nucleus inner membrane. Cytoplasmic vesicle. Secretory vesicle. Acrosome.

Miscellaneous. The primate lineage appears to have undergone gene duplication of FAM209, such that humans contain FAM209A and FAM209B.

Similarity. Belongs to the FAM209 family.

RefSeq proteins (1): NP_001013668* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027943	FAM209	Family

Pfam: PF15206

UniProt features (9 total): sequence variant 3, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JX69-F1	58.41	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): GOCC_SECRETORY_GRANULE, GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOCC_NUCLEAR_ENVELOPE, GOCC_SECRETORY_VESICLE, GOCC_ORGANELLE_INNER_MEMBRANE, GOCC_NUCLEAR_INNER_MEMBRANE, GOCC_ACROSOMAL_VESICLE, GOCC_NUCLEAR_MEMBRANE, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOCC_ORGANELLE_ENVELOPE, GSE13485_DAY3_VS_DAY21_YF17D_VACCINE_PBMC_UP, DESCARTES_MAIN_FETAL_LENS_FIBRE_CELLS, NAKAYA_PBMC_FLUMIST_AGE_18_50YO_3DY_DN

GO Biological Process (2): spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (0):

GO Cellular Component (5): acrosomal vesicle (GO:0001669), nucleus (GO:0005634), nuclear inner membrane (GO:0005637), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
secretory granule	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
nuclear membrane	1
cellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

216 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM209B	FMR1NB	Q8N0W7	511
FAM209B	BCAS4	Q8TDM0	450
FAM209B	PDHA2	P29803	446
FAM209B	PHACTR3	Q96KR7	438
FAM209B	RAB2B	Q8WUD1	417
FAM209B	ATP5F1E	P56381	379
FAM209B	TULP2	O00295	348
FAM209B	PKDREJ	Q9NTG1	348
FAM209B	ZFAND4	Q86XD8	348
FAM209B	MAGEB16	A2A368	347
FAM209B	TMCO5A	Q8N6Q1	343
FAM209B	CATSPER1	Q8NEC5	339
FAM209B	SPATA16	Q9BXB7	333
FAM209B	ATP5F1D	P30049	323
FAM209B	SLC25A3	Q00325	323
FAM209B	ATP5PD	O75947	323

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A096P2H6, A0A0D9S1R4, A2APA5, A9CBA0, P06740, P06759, P0DKU6, P0DKW1, P0DKW2, P0DKW3, P0DKW4, P0DKY3, P0DML4, P0DML5, P0DML6, P0DMN8, P0DOC4, P0DP53, P0DTG9, P0DTH0, P0DTH1, P0DTH2, P0DTH3, P0DTH4, P0DUP5, P0DUP6, P22749, P33622, P35225, P55056, P55057, P55797, Q0VCT2, Q13790, Q3SYR5, Q3ZRW9, Q5HZE8, Q5JTB6, Q5JX69, Q5JX71

Diamond homologs: A2APA5, Q5JX69, Q5JX71

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	8
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

92 predictions. Top by Δscore:

Variant	Effect	Δscore
20:56533588:AAGG:A	donor_loss	0.9900
20:56533590:GGTA:G	donor_loss	0.9900
20:56533591:G:C	donor_loss	0.9900
20:56533591:G:GG	donor_gain	0.9900
20:56536169:CA:C	acceptor_loss	0.9900
20:56536170:A:C	acceptor_loss	0.9900
20:56536171:G:GC	acceptor_loss	0.9900
20:56536170:A:AG	acceptor_gain	0.9800
20:56536171:G:GG	acceptor_gain	0.9800
20:56536171:GGA:G	acceptor_gain	0.9700
20:56536171:GGAGC:G	acceptor_gain	0.9600
20:56536166:T:TA	acceptor_gain	0.9500
20:56533589:AG:A	donor_gain	0.9200
20:56533590:GG:G	donor_gain	0.9200
20:56534313:T:G	donor_gain	0.9200
20:56534314:G:GG	donor_gain	0.9100
20:56536170:AG:A	acceptor_gain	0.9100
20:56536171:GG:G	acceptor_gain	0.9100
20:56533586:ATAAG:A	donor_gain	0.8900
20:56533587:TAAG:T	donor_gain	0.8900
20:56534318:GGAGA:G	donor_gain	0.8900
20:56536169:CAGG:C	acceptor_gain	0.8900
20:56536170:AGGA:A	acceptor_gain	0.8900
20:56536171:GGAG:G	acceptor_gain	0.8900
20:56534319:G:T	donor_gain	0.8800
20:56534330:GT:G	donor_gain	0.8600
20:56534404:C:A	donor_gain	0.8500
20:56533392:C:G	donor_gain	0.8400
20:56536172:G:C	acceptor_gain	0.8100
20:56533296:C:T	donor_gain	0.8000

AlphaMissense

1123 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:56533405:T:C	F22L	0.875
20:56533407:C:A	F22L	0.875
20:56533407:C:G	F22L	0.875
20:56533525:T:A	W62R	0.796
20:56533525:T:C	W62R	0.796
20:56533390:A:C	S17R	0.795
20:56533392:C:A	S17R	0.795
20:56533392:C:G	S17R	0.795
20:56536298:T:C	F126L	0.777
20:56536300:T:A	F126L	0.777
20:56536300:T:G	F126L	0.777
20:56533465:T:C	F42L	0.753
20:56533467:T:A	F42L	0.753
20:56533467:T:G	F42L	0.753
20:56533378:T:C	C13R	0.734
20:56533549:T:C	F70L	0.732
20:56533551:T:A	F70L	0.732
20:56533551:T:G	F70L	0.732
20:56536324:A:C	K134N	0.730
20:56536324:A:T	K134N	0.730
20:56536259:T:C	F113L	0.692
20:56536261:C:A	F113L	0.692
20:56536261:C:G	F113L	0.692
20:56536323:A:T	K134I	0.683
20:56533534:T:C	F65L	0.682
20:56533536:T:A	F65L	0.682
20:56533536:T:G	F65L	0.682
20:56533506:G:C	W55C	0.680
20:56533506:G:T	W55C	0.680
20:56533504:T:A	W55R	0.673

dbSNP variants (sampled 300 via entrez): RS1000155827 (20:56533760 A>T), RS1001317103 (20:56534170 T>C), RS1001602125 (20:56535877 A>G), RS1001827164 (20:56535759 T>C), RS1001950568 (20:56535415 A>T), RS1003627934 (20:56532069 G>A), RS1003680450 (20:56531680 G>A,C), RS1004101423 (20:56533722 G>A,T), RS1004113779 (20:56536450 T>A,C), RS1004625866 (20:56531625 A>G), RS1005241312 (20:56534925 T>G), RS1006101574 (20:56536605 G>A), RS1006621368 (20:56534422 C>G), RS1007704173 (20:56531816 G>T), RS1008026856 (20:56532144 T>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
GCST001762_730	Obesity-related traits	6.000000e-06
GCST009391_1424	Metabolite levels	4.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005116	urinary metabolite measurement
EFO:0010452	adenosine diphosphate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
pentanal	decreases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Lead	increases expression	1
Quercetin	increases expression	1
Antirheumatic Agents	decreases expression	1
Copper Sulfate	increases expression	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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