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FAM209A

gene
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Also known as dJ1153D9.3

Summary

FAM209A (family with sequence similarity 209 member A, HGNC:16100) is a protein-coding gene on chromosome 20q13.31, encoding Protein FAM209A (Q5JX71). May play a role in sperm acrosome biogenesis.

Predicted to be involved in cell differentiation and spermatogenesis. Located in extracellular exosome and nucleus.

Source: NCBI Gene 200232 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 36 total
  • MANE Select transcript: NM_001012971

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16100
Approved symbolFAM209A
Namefamily with sequence similarity 209 member A
Location20q13.31
Locus typegene with protein product
StatusApproved
AliasesdJ1153D9.3
Ensembl geneENSG00000124103
Ensembl biotypeprotein_coding
Entrez200232

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000371328, ENST00000481560

RefSeq mRNA: 1 — MANE Select: NM_001012971 NM_001012971

CCDS: CCDS33493

Canonical transcript exons

ENST00000371328 — 2 exons

ExonStartEnd
ENSE000014549555652580456526152
ENSE000017462235652474456525057

Expression profiles

Bgee: expression breadth ubiquitous, 125 present calls, max score 97.65.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453397.65gold quality
right testisUBERON:000453497.35gold quality
testisUBERON:000047397.17gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047392.02gold quality
bloodUBERON:000017878.64gold quality
bone marrowUBERON:000237176.71gold quality
granulocyteCL:000009475.58gold quality
bone marrow cellCL:000209270.55gold quality
spleenUBERON:000210670.04gold quality
monocyteCL:000057669.55gold quality
leukocyteCL:000073867.69gold quality
lymph nodeUBERON:000002964.50gold quality
skin of legUBERON:000151164.40gold quality
zone of skinUBERON:000001463.39gold quality
skin of abdomenUBERON:000141662.28gold quality
small intestine Peyer’s patchUBERON:000345461.81gold quality
subcutaneous adipose tissueUBERON:000219061.34gold quality
upper lobe of left lungUBERON:000895260.77gold quality
vermiform appendixUBERON:000115460.31gold quality
fundus of stomachUBERON:000116060.24gold quality
small intestineUBERON:000210860.21gold quality
olfactory segment of nasal mucosaUBERON:000538660.19gold quality
adipose tissueUBERON:000101359.10gold quality
mucosa of stomachUBERON:000119958.72gold quality
right lobe of liverUBERON:000111458.49gold quality
mucosa of transverse colonUBERON:000499158.14gold quality
tonsilUBERON:000237257.99gold quality
body of stomachUBERON:000116157.80gold quality
right uterine tubeUBERON:000130257.45gold quality
descending thoracic aortaUBERON:000234557.26gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no1.54

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusFam209ENSMUSG00000027505
rattus_norvegicusFam209ENSRNOG00000005235

Paralogs (1): FAM209B (ENSG00000213714)

Protein

Protein identifiers

Protein FAM209A — Q5JX71 (reviewed: Q5JX71)

All UniProt accessions (1): Q5JX71

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in sperm acrosome biogenesis.

Subunit / interactions. Interacts with DPY19L2. Interacts with CYLC1; the interaction may be relevant for proper acrosome attachment to the nuclear envelope.

Subcellular location. Nucleus inner membrane.

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_001012989* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR027943FAM209Family

Pfam: PF15206

UniProt features (13 total): sequence variant 5, topological domain 2, signal peptide 1, chain 1, sequence conflict 1, transmembrane region 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5JX71-F158.990.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOCC_NUCLEAR_ENVELOPE, GOCC_ORGANELLE_INNER_MEMBRANE, GOCC_NUCLEAR_INNER_MEMBRANE, GOCC_NUCLEAR_MEMBRANE, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, VANASSE_BCL2_TARGETS_UP, GOCC_ORGANELLE_ENVELOPE, E2F3_UP.V1_DN, DESCARTES_MAIN_FETAL_CLC_IL5RA_POSITIVE_CELLS, DESCARTES_FETAL_HEART_CLC_IL5RA_POSITIVE_CELLS, NAKAYA_PBMC_FLUMIST_AGE_18_50YO_3DY_DN, GOBP_SEXUAL_REPRODUCTION, GOBP_REPRODUCTIVE_PROCESS

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

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nuclear inner membrane (GO:0005637), extracellular exosome (GO:0070062), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
developmental process involved in reproduction1
male gamete generation1
cellular developmental process1
binding1
intracellular membrane-bounded organelle1
organelle inner membrane1
nuclear membrane1
extracellular vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

350 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FAM209ATMCO5AQ8N6Q1705
FAM209AC9orf43Q8TAL5667
FAM209ASPATA31G1Q5VYM1647
FAM209AREDIC1Q86WS4627
FAM209ASPATA16Q9BXB7627
FAM209AMAGEB16A2A368626
FAM209AZFAND4Q86XD8590
FAM209ATULP2O00295564
FAM209ASPACA9Q96E40562
FAM209APKDREJQ9NTG1561
FAM209APLCZ1Q86YW0539
FAM209ATMCO2Q7Z6W1527
FAM209ACCDC187A0A096LP49526
FAM209ACXorf65A6NEN9517
FAM209ATMEM179BQ7Z7N9507

IntAct

694 interactions, top by confidence:

ABTypeScore
FAM209AUBASH3Bpsi-mi:“MI:0915”(physical association)0.590
BDNFFAM209Apsi-mi:“MI:0915”(physical association)0.560
HMOX2FAM209Apsi-mi:“MI:0915”(physical association)0.000
TMEM120AFAM209Apsi-mi:“MI:0915”(physical association)0.000
AQP3FAM209Apsi-mi:“MI:0915”(physical association)0.000
TMBIM6FAM209Apsi-mi:“MI:0915”(physical association)0.000
C11orf24FAM209Apsi-mi:“MI:0915”(physical association)0.000
CLEC4GFAM209Apsi-mi:“MI:0915”(physical association)0.000
IGFBP5FAM209Apsi-mi:“MI:0915”(physical association)0.000
ERMP1FAM209Apsi-mi:“MI:0915”(physical association)0.000
TMEM229BFAM209Apsi-mi:“MI:0915”(physical association)0.000
SMIM1FAM209Apsi-mi:“MI:0915”(physical association)0.000
WFDC2FAM209Apsi-mi:“MI:0915”(physical association)0.000
SLC35E3FAM209Apsi-mi:“MI:0915”(physical association)0.000
NCR3FAM209Apsi-mi:“MI:0915”(physical association)0.000
VKORC1FAM209Apsi-mi:“MI:0915”(physical association)0.000
B4GALNT2FAM209Apsi-mi:“MI:0915”(physical association)0.000
KIR2DL3FAM209Apsi-mi:“MI:0915”(physical association)0.000
BTN2A2FAM209Apsi-mi:“MI:0915”(physical association)0.000
GPR37L1FAM209Apsi-mi:“MI:0915”(physical association)0.000
TWSG1FAM209Apsi-mi:“MI:0915”(physical association)0.000
GASTFAM209Apsi-mi:“MI:0915”(physical association)0.000
FAM209Apsi-mi:“MI:0915”(physical association)0.000
CMTM7FAM209Apsi-mi:“MI:0915”(physical association)0.000
GIMAP1FAM209Apsi-mi:“MI:0915”(physical association)0.000
FAM20BFAM209Apsi-mi:“MI:0915”(physical association)0.000
PLPP4FAM209Apsi-mi:“MI:0915”(physical association)0.000
PGLYRP3FAM209Apsi-mi:“MI:0915”(physical association)0.000
FAM3CFAM209Apsi-mi:“MI:0915”(physical association)0.000
RUSF1FAM209Apsi-mi:“MI:0915”(physical association)0.000

BioGRID (263): UBASH3B (Affinity Capture-MS), UBASH3B (Affinity Capture-MS), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid), FAM209A (Two-hybrid)

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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 180 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Insertion of tail-anchored proteins into the endoplasmic reticulum membrane629.1×1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance31
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

231 predictions. Top by Δscore:

VariantEffectΔscore
20:56517202:GTG:Gdonor_loss1.0000
20:56517203:T:Adonor_loss1.0000
20:56518085:A:AGacceptor_gain1.0000
20:56518086:G:GGacceptor_gain1.0000
20:56518086:GCA:Gacceptor_gain1.0000
20:56518086:GCAA:Gacceptor_gain1.0000
20:56518086:GCAAT:Gacceptor_gain1.0000
20:56518082:TCTAG:Tacceptor_loss0.9900
20:56518085:A:Gacceptor_loss0.9900
20:56518086:G:Aacceptor_loss0.9900
20:56518086:GC:Gacceptor_gain0.9900
20:56525056:AGGTA:Adonor_loss0.9900
20:56525057:GGTA:Gdonor_loss0.9900
20:56517202:G:GGdonor_gain0.9800
20:56518088:A:AGacceptor_gain0.9800
20:56525059:T:Gdonor_loss0.9800
20:56525799:GACA:Gacceptor_loss0.9800
20:56525801:CAG:Cacceptor_loss0.9800
20:56525802:A:AGacceptor_gain0.9800
20:56525803:G:GGacceptor_gain0.9800
20:56518088:AAT:Aacceptor_gain0.9700
20:56525798:T:Aacceptor_gain0.9700
20:56525803:GGA:Gacceptor_gain0.9700
20:56525803:GGAGC:Gacceptor_gain0.9700
20:56525058:G:GGdonor_gain0.9600
20:56517933:T:Aacceptor_gain0.9500
20:56518089:A:Gacceptor_gain0.9500
20:56525802:AG:Aacceptor_gain0.9300
20:56525803:GG:Gacceptor_gain0.9300
20:56517255:TGGCC:Tdonor_gain0.9000

AlphaMissense

1124 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:56524872:T:CF22L0.861
20:56524874:C:AF22L0.861
20:56524874:C:GF22L0.861
20:56525955:A:TK134I0.842
20:56524992:T:AW62R0.823
20:56524992:T:CW62R0.823
20:56524857:A:CS17R0.794
20:56524859:C:AS17R0.794
20:56524859:C:GS17R0.794
20:56525930:T:CF126L0.788
20:56525932:T:AF126L0.788
20:56525932:T:GF126L0.788
20:56525956:A:CK134N0.776
20:56525956:A:TK134N0.776
20:56524845:T:CC13R0.756
20:56524932:T:CF42L0.717
20:56524934:T:AF42L0.717
20:56524934:T:GF42L0.717
20:56525016:T:CF70L0.717
20:56525018:T:AF70L0.717
20:56525018:T:GF70L0.717
20:56525922:T:CL123P0.706
20:56524971:T:AW55R0.697
20:56524971:T:CW55R0.697
20:56525891:T:CF113L0.697
20:56525893:C:AF113L0.697
20:56525893:C:GF113L0.697
20:56524973:G:CW55C0.678
20:56524973:G:TW55C0.678
20:56524986:T:AW60R0.664

dbSNP variants (sampled 300 via entrez): RS1000002174 (20:56527567 C>T), RS1000155827 (20:56533760 A>T), RS1000161665 (20:56526733 G>A), RS1000562973 (20:56524050 C>T), RS1000892213 (20:56527619 G>A), RS1001016929 (20:56523864 G>A), RS1001223295 (20:56528957 C>T), RS1001619857 (20:56529056 A>G), RS1001671982 (20:56528803 G>A,T), RS1001743850 (20:56524013 T>A), RS1001938572 (20:56525413 A>G), RS1001956663 (20:56530387 G>C,T), RS1002002793 (20:56530091 C>A,T), RS1002091852 (20:56530884 C>T), RS1002477423 (20:56525228 G>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):

StudyTraitp-value
GCST002579_14Heschl’s gyrus morphology8.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
versicolorin Aincreases expression1
di-n-butylphosphoric acidaffects expression1
jinfukangaffects cotreatment, decreases expression1
Cisplatinaffects cotreatment, decreases expression1
Plant Oilsincreases expression1
Quercetinincreases expression1
Silicon Dioxideincreases expression1
Tobacco Smoke Pollutionincreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot