FAM9B

Summary

FAM9B (family with sequence similarity 9 member B, HGNC:18404) is a protein-coding gene on chromosome Xp22.31, encoding Protein FAM9B (Q8IZU0). May play a role in meiosis.

This gene is a member of a gene family which arose through duplication on the X chromosome. The encoded protein may be localized to the nucleus as the protein contains several nuclear localization signals, and has similarity to a synaptonemal complex protein.

Source: NCBI Gene 171483 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 40 total — 1 pathogenic
• MANE Select transcript: NM_205849

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18404
Approved symbol	FAM9B
Name	family with sequence similarity 9 member B
Location	Xp22.31
Locus type	gene with protein product
Status	Approved
Aliases	TEX39B
Ensembl gene	ENSG00000177138
Ensembl biotype	protein_coding
OMIM	300478
Entrez	171483

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000327220, ENST00000362066, ENST00000428477, ENST00000461107, ENST00000472522, ENST00000494744, ENST00000651278

RefSeq mRNA: 1 — MANE Select: NM_205849 NM_205849

CCDS: CCDS14132

Canonical transcript exons

ENST00000327220 — 9 exons

Exon	Start	End
ENSE00001433882	9033852	9034127
ENSE00001897452	9024232	9025377
ENSE00003466809	9032959	9033075
ENSE00003472429	9025484	9025583
ENSE00003522410	9027868	9027966
ENSE00003634219	9032130	9032161
ENSE00003659377	9032341	9032461
ENSE00003682132	9029307	9029418
ENSE00003693246	9030261	9030360

Expression profiles

Bgee: expression breadth broad, 74 present calls, max score 80.93.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.93	gold quality
right lobe of liver	UBERON:0001114	72.80	gold quality
right testis	UBERON:0004534	72.78	gold quality
left testis	UBERON:0004533	72.12	gold quality
testis	UBERON:0000473	71.52	gold quality
buccal mucosa cell	CL:0002336	68.10	gold quality
body of uterus	UBERON:0009853	67.17	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.46	gold quality
liver	UBERON:0002107	61.77	gold quality
smooth muscle tissue	UBERON:0001135	61.01	gold quality
myometrium	UBERON:0001296	55.63	gold quality
uterus	UBERON:0000995	53.17	gold quality
stromal cell of endometrium	CL:0002255	51.58	silver quality
prostate gland	UBERON:0002367	51.48	gold quality
sural nerve	UBERON:0015488	51.35	gold quality
endometrium	UBERON:0001295	49.87	gold quality
cerebellar vermis	UBERON:0004720	48.63	gold quality
granulocyte	CL:0000094	47.96	silver quality
hypothalamus	UBERON:0001898	45.59	gold quality
female reproductive system	UBERON:0000474	44.66	gold quality
oocyte	CL:0000023	43.92	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
monocyte	CL:0000576	43.15	silver quality
corpus epididymis	UBERON:0004359	42.98	gold quality
adult organism	UBERON:0007023	42.85	gold quality
blood	UBERON:0000178	42.83	gold quality
muscle tissue	UBERON:0002385	42.70	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
quadriceps femoris	UBERON:0001377	42.39	gold quality
lymph node	UBERON:0000029	42.13	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

53 targeting FAM9B, 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-3064-3P	100.00	70.09	1254
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-377-5P	99.70	65.28	712
HSA-MIR-6086	99.70	65.38	699
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-1303	99.65	69.77	1662
HSA-MIR-5689	99.50	71.26	1154
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-18A-5P	99.29	71.05	806
HSA-MIR-18B-5P	99.29	71.05	806
HSA-MIR-6719-3P	99.29	67.78	1387

Literature-anchored findings (GeneRIF, showing 1)

• Expressed exclusively in testis; protein is located in the nucleus. (PMID:12213195)

Cross-species orthologs

21 orthologs

Organism	Symbol	Gene ID
danio_rerio	sycp3	ENSDARG00000013438
mus_musculus	Xlr4c	ENSMUSG00000031362
mus_musculus	Xlr3a	ENSMUSG00000057836
mus_musculus	Xlr3c	ENSMUSG00000058147
mus_musculus	Xlr5a	ENSMUSG00000058328
mus_musculus	Xlr5c	ENSMUSG00000067764
mus_musculus	Xlr4b	ENSMUSG00000067768
mus_musculus	Xlr5b	ENSMUSG00000072479
mus_musculus	Xlr3b	ENSMUSG00000073125
mus_musculus	Gm14692	ENSMUSG00000079577
mus_musculus	Gm1140	ENSMUSG00000079578
mus_musculus	Xlr4a	ENSMUSG00000079845
rattus_norvegicus	Xlr5c	ENSRNOG00000050177
rattus_norvegicus	Xlr4a	ENSRNOG00000055822
rattus_norvegicus	Fam9cl1	ENSRNOG00000062315
rattus_norvegicus	LOC100911047	ENSRNOG00000064693
rattus_norvegicus	LOC100911047	ENSRNOG00000068104
rattus_norvegicus	Fam9c	ENSRNOG00000069253
rattus_norvegicus		ENSRNOG00000075733
rattus_norvegicus		ENSRNOG00000087898
rattus_norvegicus		ENSRNOG00000088563

Paralogs (3): SYCP3 (ENSG00000139351), FAM9A (ENSG00000183304), FAM9C (ENSG00000187268)

Protein

Protein identifiers

Protein FAM9B — Q8IZU0 (reviewed: Q8IZU0)

All UniProt accessions (1): Q8IZU0

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in meiosis.

Subcellular location. Nucleus. Cytoplasm. Chromosome.

Tissue specificity. Expressed in testis and ovary (at protein level).

Similarity. Belongs to the XLR/SYCP3 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IZU0-1	1	yes
Q8IZU0-2	2

RefSeq proteins (1): NP_995321* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006888	XLR/SYCP3/FAM9_dom	Domain
IPR051443	XLR/SYCP3	Family

Pfam: PF04803

UniProt features (7 total): compositionally biased region 3, splice variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IZU0-F1	79.88	0.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MEIOTIC_CELL_CYCLE, GOCC_NUCLEAR_CHROMOSOME, GOCC_CONDENSED_NUCLEAR_CHROMOSOME, SENESE_HDAC1_AND_HDAC2_TARGETS_UP, chrXp22, GOCC_SYNAPTONEMAL_STRUCTURE, DIDO1_TARGET_GENES, HES2_TARGET_GENES, MAFG_TARGET_GENES, MIR4778_3P, MIR6740_3P, MIR18A_5P_MIR18B_5P

GO Biological Process (2): spermatid development (GO:0007286), meiotic cell cycle (GO:0051321)

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

GO Cellular Component (5): synaptonemal complex (GO:0000795), nucleus (GO:0005634), nucleoplasm (GO:0005654), chromosome (GO:0005694), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
germ cell development	1
spermatid differentiation	1
cell cycle	1
sexual reproduction	1
reproductive process	1
meiotic nuclear division	1
binding	1
synaptonemal structure	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular membraneless organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

736 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM9B	Q15513	Q15513	518
FAM9B	SHBG	P04278	446
FAM9B	NUTM2F	A1L443	431
FAM9B	ST8SIA5	O15466	421
FAM9B	IZUMO3	Q5VZ72	415
FAM9B	JMJD1C	Q15652	414
FAM9B	FAM47C	Q5HY64	398
FAM9B	ST6GALNAC4	Q9H4F1	387
FAM9B	CPXCR1	Q8N123	374
FAM9B	ANOS1	P23352	370
FAM9B	CMC4	P56277	369
FAM9B	VCX3B	Q9H321	358
FAM9B	ATP6V0D1	P12953	353
FAM9B	AGRP	O00253	353
FAM9B	ADAT1	Q9BUB4	333

IntAct

507 interactions, top by confidence:

A	B	Type	Score
FAM9B	XRCC4	psi-mi:“MI:0915”(physical association)	0.870
XRCC4	FAM9B	psi-mi:“MI:0915”(physical association)	0.870
PRPF3	FAM9B	psi-mi:“MI:0915”(physical association)	0.810
FAM9B	PRPF3	psi-mi:“MI:0915”(physical association)	0.810
FAM9B	PHYH	psi-mi:“MI:0915”(physical association)	0.780
FAM9B	SMN1	psi-mi:“MI:0915”(physical association)	0.780
FAM9B	CCDC106	psi-mi:“MI:0915”(physical association)	0.780
FAM9B	CHRAC1	psi-mi:“MI:0915”(physical association)	0.780
SMN1	FAM9B	psi-mi:“MI:0915”(physical association)	0.780
HAPSTR1	FAM9B	psi-mi:“MI:0915”(physical association)	0.740
SDCBP	FAM9B	psi-mi:“MI:0915”(physical association)	0.720
FAM9B	NDUFB10	psi-mi:“MI:0915”(physical association)	0.720
FAM9B	SLPI	psi-mi:“MI:0915”(physical association)	0.720
FAM9B	SDCBP	psi-mi:“MI:0915”(physical association)	0.720
SLPI	FAM9B	psi-mi:“MI:0915”(physical association)	0.720
FAM9B	FCHSD2	psi-mi:“MI:0915”(physical association)	0.670
TUFM	FAM9B	psi-mi:“MI:0915”(physical association)	0.670
FAM9B	FASTKD3	psi-mi:“MI:0915”(physical association)	0.670
TGFBI	FAM9B	psi-mi:“MI:0915”(physical association)	0.670
FAM9B	SNX20	psi-mi:“MI:0915”(physical association)	0.670
FAM9B	MYG1	psi-mi:“MI:0915”(physical association)	0.670
CDC42EP4	FAM9B	psi-mi:“MI:0915”(physical association)	0.670
CEP95	FAM9B	psi-mi:“MI:0915”(physical association)	0.670
FAM9B	FERD3L	psi-mi:“MI:0915”(physical association)	0.670
SYT17	FAM9B	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (188): FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid), FAM9B (Two-hybrid)

ESM2 similar proteins: A7TJT3, B3EWV0, C0HLQ3, O31159, O66093, O66096, O91083, P0C1J9, P0C1K3, P0C1K4, P0C8M3, P0CA74, P21016, P24360, P33868, P52531, P80745, P82331, P83602, P84712, P86298, P86299, P86300, P86301, P86302, P86305, P86307, P86309, P86310, P86688, Q02838, Q1A264, Q27976, Q44160, Q46490, Q54C30, Q54KW6, Q54PY5, Q54V15, Q54X31

Diamond homologs: P05531, P70281, Q3T0E2, Q4R764, Q60547, Q60595, Q61806, Q63520, Q6P205, Q8IZU0, Q8IZU3, Q8IZT9, Q8IZU1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	30
Likely benign	3
Benign	2

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
816281	GRCh37/hg19 Xp22.33-22.12(chrX:1240318-20986848)x2	Pathogenic

SpliceAI

953 predictions. Top by Δscore:

Variant	Effect	Δscore
X:9027963:TTCT:T	acceptor_gain	1.0000
X:9027965:CT:C	acceptor_gain	1.0000
X:9027967:C:CC	acceptor_gain	1.0000
X:9027976:C:T	acceptor_gain	1.0000
X:9029302:CCAA:C	donor_gain	1.0000
X:9029305:A:AC	donor_gain	1.0000
X:9029306:C:CC	donor_gain	1.0000
X:9029306:CA:C	donor_gain	1.0000
X:9029306:CAA:C	donor_gain	1.0000
X:9029317:T:TA	donor_gain	1.0000
X:9029318:C:A	donor_gain	1.0000
X:9029326:C:CA	donor_gain	1.0000
X:9029341:T:TA	donor_gain	1.0000
X:9029415:CTGC:C	acceptor_gain	1.0000
X:9029416:TGC:T	acceptor_gain	1.0000
X:9029417:GC:G	acceptor_gain	1.0000
X:9029418:CC:C	acceptor_gain	1.0000
X:9029419:C:CC	acceptor_gain	1.0000
X:9029419:C:CG	acceptor_loss	1.0000
X:9029420:T:A	acceptor_loss	1.0000
X:9030370:CAGT:C	acceptor_gain	1.0000
X:9030371:A:T	acceptor_gain	1.0000
X:9030373:T:C	acceptor_gain	1.0000
X:9030373:T:TC	acceptor_gain	1.0000
X:9030377:A:AC	acceptor_gain	1.0000
X:9030380:G:GC	acceptor_gain	1.0000
X:9030384:A:AC	acceptor_gain	1.0000
X:9032329:TAA:T	donor_gain	1.0000
X:9032330:AAA:A	donor_gain	1.0000
X:9032335:CTTTA:C	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1001299967 (X:9023944 C>T), RS1001351418 (X:9034481 T>G), RS1001585686 (X:9024291 G>A,C), RS1003524488 (X:9026454 G>A), RS1005544430 (X:9031827 C>T), RS1005670166 (X:9027005 G>A,T), RS1005957421 (X:9024682 T>C), RS1006032211 (X:9026513 G>A), RS1006126546 (X:9034636 A>G,T), RS1006449729 (X:9035867 C>A), RS1006552655 (X:9035283 T>A,C), RS1007504537 (X:9033922 C>T), RS1007651407 (X:9036006 G>A), RS1007824024 (X:9034171 G>A,C), RS1007923571 (X:9025218 G>A)

Disease associations

OMIM: gene MIM:300478 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST001653_4	Androgen levels	2.000000e-08
GCST003983_43	Male-pattern baldness	4.000000e-08
GCST003994_14	Age at voice drop	3.000000e-09
GCST005116_57	Male-pattern baldness	4.000000e-13
GCST005984_21	Glomerular filtration rate	5.000000e-09
GCST005985_11	Creatinine levels	5.000000e-09
GCST005994_15	Hematocrit	3.000000e-08
GCST005995_5	Hemoglobin	4.000000e-08
GCST006288_418	Heel bone mineral density	5.000000e-17
GCST006288_698	Heel bone mineral density	6.000000e-07
GCST006979_838	Heel bone mineral density	1.000000e-24
GCST009391_1044	Metabolite levels	2.000000e-07

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004908	testosterone measurement
EFO:0007888	age at voice drop
EFO:0004348	hematocrit
EFO:0004509	hemoglobin measurement
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
bufotalin	increases expression	1
propionaldehyde	increases expression	1
CGP 52608	increases reaction, affects binding	1
Valproic Acid	increases methylation	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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