FAM13B

Summary

FAM13B (family with sequence similarity 13 member B, HGNC:1335) is a protein-coding gene on chromosome 5q31.2, encoding Protein FAM13B (Q9NYF5).

Predicted to enable GTPase activator activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol.

Source: NCBI Gene 51306 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 137 total
• MANE Select transcript: NM_001385994

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1335
Approved symbol	FAM13B
Name	family with sequence similarity 13 member B
Location	5q31.2
Locus type	gene with protein product
Status	Approved
Aliases	N61, KHCHP, ARHGAP49
Ensembl gene	ENSG00000031003
Ensembl biotype	protein_coding
OMIM	609371
Entrez	51306

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 16 protein_coding, 3 retained_intron

ENST00000033079, ENST00000420893, ENST00000425075, ENST00000502471, ENST00000505281, ENST00000505961, ENST00000508403, ENST00000509596, ENST00000510804, ENST00000513640, ENST00000514310, ENST00000689681, ENST00000874970, ENST00000874971, ENST00000874972, ENST00000921477, ENST00000956469, ENST00000956470, ENST00000956471

RefSeq mRNA: 25 — MANE Select: NM_001385994 NM_001101800, NM_001101801, NM_001385866, NM_001385867, NM_001385868, NM_001385869, NM_001385870, NM_001385872, NM_001385873, NM_001385874, NM_001385921, NM_001385976, NM_001385977, NM_001385978, NM_001385979, NM_001385980, NM_001385991, NM_001385992, NM_001385994, NM_001385995, NM_001385996, NM_001385997, NM_001385998, NM_001385999, NM_016603

CCDS: CCDS4195, CCDS47269, CCDS47270, CCDS93788

Canonical transcript exons

ENST00000689681 — 24 exons

Exon	Start	End
ENSE00000764166	137941944	137942045
ENSE00000764178	137943133	137943216
ENSE00000764182	137945902	137945997
ENSE00000764192	137946228	137946311
ENSE00000764205	137948955	137949184
ENSE00000764219	137952628	137952709
ENSE00000764223	137953336	137953465
ENSE00000764246	137959616	137959763
ENSE00000764272	137960166	137960214
ENSE00001086057	138011008	138011149
ENSE00001130368	137962405	137962469
ENSE00001130372	137985257	137985389
ENSE00001130382	137987461	137987616
ENSE00001130389	137988274	137988315
ENSE00001130396	138006990	138007147
ENSE00001195996	137942875	137943038
ENSE00001196051	138011768	138011945
ENSE00001255108	137954166	137954376
ENSE00001342011	138021031	138021197
ENSE00001725085	137956477	137956542
ENSE00001921816	137937960	137940348
ENSE00003646132	138018302	138018514
ENSE00003799660	138018955	138019146
ENSE00003933095	138032782	138033079

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 95.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.6391 / max 311.6793, expressed in 1818 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
63665	22.5213	1817
63666	1.6840	1003
63664	1.0640	590
63663	0.1806	66
63667	0.0976	39
63668	0.0916	39

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
blood vessel layer	UBERON:0004797	95.62	gold quality
calcaneal tendon	UBERON:0003701	95.37	gold quality
germinal epithelium of ovary	UBERON:0001304	95.10	gold quality
cauda epididymis	UBERON:0004360	95.05	gold quality
palpebral conjunctiva	UBERON:0001812	94.37	gold quality
adrenal tissue	UBERON:0018303	94.37	gold quality
seminal vesicle	UBERON:0000998	94.28	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.07	gold quality
parietal pleura	UBERON:0002400	93.97	gold quality
sural nerve	UBERON:0015488	93.84	gold quality
pleura	UBERON:0000977	93.62	gold quality
visceral pleura	UBERON:0002401	93.47	gold quality
endothelial cell	CL:0000115	93.36	gold quality
secondary oocyte	CL:0000655	93.30	gold quality
urethra	UBERON:0000057	93.25	gold quality
superficial temporal artery	UBERON:0001614	92.73	gold quality
eye	UBERON:0000970	92.67	gold quality
metanephric glomerulus	UBERON:0004736	92.28	gold quality
renal glomerulus	UBERON:0000074	92.25	gold quality
right coronary artery	UBERON:0001625	92.14	gold quality
trigeminal ganglion	UBERON:0001675	92.01	gold quality
primary visual cortex	UBERON:0002436	91.70	gold quality
epithelium of mammary gland	UBERON:0003244	91.55	gold quality
mammary duct	UBERON:0001765	91.52	gold quality
right adrenal gland cortex	UBERON:0035827	91.24	gold quality
middle temporal gyrus	UBERON:0002771	90.97	gold quality
dorsal root ganglion	UBERON:0000044	90.93	gold quality
heart right ventricle	UBERON:0002080	90.93	gold quality
descending thoracic aorta	UBERON:0002345	90.85	gold quality
mucosa of stomach	UBERON:0001199	90.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

129 targeting FAM13B, 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-656-3P	100.00	72.15	2788
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-607	99.97	73.62	5593

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam13b	ENSDARG00000076779
mus_musculus	Fam13b	ENSMUSG00000036501
rattus_norvegicus	Fam13b	ENSRNOG00000020384
drosophila_melanogaster	CG6424	FBGN0028494

Paralogs (2): FAM13A (ENSG00000138640), FAM13C (ENSG00000148541)

Protein

Protein identifiers

Protein FAM13B — Q9NYF5 (reviewed: Q9NYF5)

Alternative names: GAP-like protein N61

All UniProt accessions (8): A0A2X0SG06, A0A8I5KSB9, D6RAT6, D6RBJ3, D6RCA0, D6RDL7, D6RE97, Q9NYF5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM13 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NYF5-1	1	yes
Q9NYF5-2	2
Q9NYF5-3	3

RefSeq proteins (25): NP_001095270, NP_001095271, NP_001372795, NP_001372796, NP_001372797, NP_001372798, NP_001372799, NP_001372801, NP_001372802, NP_001372803, NP_001372850, NP_001372905, NP_001372906, NP_001372907, NP_001372908, NP_001372909, NP_001372920, NP_001372921, NP_001372923, NP_001372924, NP_001372925, NP_001372926, NP_001372927, NP_001372928, NP_057687 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000198	RhoGAP_dom	Domain
IPR008936	Rho_GTPase_activation_prot	Homologous_superfamily
IPR039102	FAM13	Family
IPR059029	FAM13A_dom	Domain

Pfam: PF00620, PF26116

UniProt features (12 total): splice variant 3, region of interest 2, compositionally biased region 2, chain 1, domain 1, sequence variant 1, sequence conflict 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NYF5-F1	62.70	0.23

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 62 (arginine finger; crucial for gtp hydrolysis by stabilizing the transition state)

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-9013148	CDC42 GTPase cycle
R-HSA-9013149	RAC1 GTPase cycle

MSigDB gene sets: 195 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, TGGTGCT_MIR29A_MIR29B_MIR29C, RNGTGGGC_UNKNOWN, TGCGCANK_UNKNOWN, CMYB_01, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GGGTGGRR_PAX4_03, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, USF_01, HEN1_01, WTGAAAT_UNKNOWN, MYB_Q3, MAF_Q6, USF_02, ZHANG_BREAST_CANCER_PROGENITORS_UP

GO Biological Process (2): signal transduction (GO:0007165), regulation of small GTPase mediated signal transduction (GO:0051056)

GO Molecular Function (1): GTPase activator activity (GO:0005096)

GO Cellular Component (1): cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RHO GTPase cycle	2

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
small GTPase-mediated signal transduction	1
regulation of intracellular signal transduction	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

808 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM13B	RASA1	P20936	566
FAM13B	PKD2L2	Q9NZM6	541
FAM13B	RETREG1	Q9H6L5	517
FAM13B	SPATA24	Q86W54	513
FAM13B	KCNJ5-AS1	Q8TAV5	506
FAM13B	SH3PXD2A	Q5TCZ1	503
FAM13B	SMIM33	A0A1B0GW64	499
FAM13B	NME5	P56597	487
FAM13B	CANX	P27824	478
FAM13B	TMEM184C	Q9NVA4	469
FAM13B	RASGEF1C	Q8N431	465
FAM13B	FAM53C	Q9NYF3	447
FAM13B	DNAJC18	Q9H819	445
FAM13B	NTMT2	Q5VVY1	440
FAM13B	WNT8A	Q9H1J5	421

IntAct

6 interactions, top by confidence:

A	B	Type	Score
FAM13B	FOXO1	psi-mi:“MI:0915”(physical association)	0.400
FAM13B	AGTR1	psi-mi:“MI:0915”(physical association)	0.370
YWHAE	FAM13B	psi-mi:“MI:0915”(physical association)	0.000
FAM13B	YWHAG	psi-mi:“MI:0915”(physical association)	0.000
WNK1	FAM13B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (30): FAM13B (Two-hybrid), FAM13B (Affinity Capture-RNA), FAM13B (Protein-RNA), FAM13B (Two-hybrid), FAM13B (FRET), FAM13B (FRET), AHCYL1 (Affinity Capture-MS), ATP5I (Affinity Capture-MS), CHCHD3 (Affinity Capture-MS), HIGD1A (Affinity Capture-MS), PAM16 (Affinity Capture-MS), PPP2CA (Affinity Capture-MS), PPP2R1A (Affinity Capture-MS), QPCTL (Affinity Capture-MS), SSR4 (Affinity Capture-MS)

ESM2 similar proteins: A0JM98, A1L1H3, B7ZS37, D2H3M0, D3ZF42, E1BPH3, E2QTD3, F6YVB9, O75113, O88866, P62287, P62288, Q01804, Q13129, Q1L981, Q2T9I9, Q5H9M0, Q5HZN1, Q5QJC4, Q5SW75, Q5T5J6, Q5VCS6, Q5XIS7, Q5ZIX8, Q5ZKI7, Q5ZLE9, Q61194, Q63679, Q6A037, Q6DJS0, Q6GQJ2, Q6IE81, Q6IE82, Q6IFT4, Q6IVY4, Q6NRK3, Q6PCM1, Q6PJP8, Q6PUR7, Q6YI93

Diamond homologs: A0A0G2JTR4, A2AB59, A2RUV4, A4IF90, A4II46, A6QNS3, A6X8Z5, A7KAX9, A8WRJ2, B2RTY4, B5DFQ4, D3ZFJ3, D3ZZN9, E7EZG2, E7F3F0, F1LXF1, O14559, O43052, O54834, O74360, O94466, P11274, P15882, P30337, P34288, P35688, P42331, P46941, P52757, P55194, P98171, Q03070, Q08DP6, Q10164, Q12979, Q13459, Q17QN0, Q20498, Q2M1Z3, Q3UIA2

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
FAM13B	“down-regulates activity”	RAC1	“gtpase-activating protein”
FAM13B	“down-regulates activity”	CDC42	“gtpase-activating protein”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	107
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4134 predictions. Top by Δscore:

Variant	Effect	Δscore
5:137941922:A:AC	donor_gain	1.0000
5:137941923:A:C	donor_gain	1.0000
5:137941939:CAAA:C	donor_loss	1.0000
5:137941940:AAACC:A	donor_loss	1.0000
5:137941941:AACCT:A	donor_loss	1.0000
5:137941942:ACC:A	donor_loss	1.0000
5:137941946:T:TA	donor_gain	1.0000
5:137942041:CAGGC:C	acceptor_gain	1.0000
5:137942042:AGGCC:A	acceptor_loss	1.0000
5:137942044:GCC:G	acceptor_loss	1.0000
5:137942045:CCT:C	acceptor_loss	1.0000
5:137942046:C:CC	acceptor_gain	1.0000
5:137942046:CTAGA:C	acceptor_loss	1.0000
5:137942047:T:C	acceptor_loss	1.0000
5:137942869:A:AC	donor_gain	1.0000
5:137942870:C:CC	donor_gain	1.0000
5:137942870:CATA:C	donor_gain	1.0000
5:137942871:ATAC:A	donor_loss	1.0000
5:137942873:A:AC	donor_gain	1.0000
5:137942873:ACA:A	donor_loss	1.0000
5:137942874:C:CA	donor_gain	1.0000
5:137942874:CA:C	donor_gain	1.0000
5:137942874:CAT:C	donor_gain	1.0000
5:137942874:CATAG:C	donor_gain	1.0000
5:137942895:TG:T	donor_gain	1.0000
5:137943034:TCCTC:T	acceptor_gain	1.0000
5:137943035:CCTCC:C	acceptor_gain	1.0000
5:137943036:CTC:C	acceptor_gain	1.0000
5:137943037:TC:T	acceptor_gain	1.0000
5:137943038:CC:C	acceptor_gain	1.0000

AlphaMissense

6267 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:137946259:A:G	L716P	1.000
5:137946271:A:G	L712P	1.000
5:137952654:A:G	L613P	1.000
5:138011795:G:T	A174D	1.000
5:138018346:A:T	V109D	1.000
5:138018358:A:G	L105P	1.000
5:138018367:A:G	L102P	1.000
5:138018379:A:G	L98P	1.000
5:138018382:A:G	L97P	1.000
5:138018384:G:C	S96R	1.000
5:138018384:G:T	S96R	1.000
5:138018386:T:G	S96R	1.000
5:138018391:G:T	A94D	1.000
5:138018418:A:G	L85S	1.000
5:138018451:C:G	R74P	1.000
5:138018454:A:G	L73P	1.000
5:138018478:C:A	G65V	1.000
5:138018478:C:T	G65E	1.000
5:138018479:C:G	G65R	1.000
5:138018479:C:T	G65R	1.000
5:138018490:A:G	F61S	1.000
5:138018966:A:T	I49N	1.000
5:138018987:A:T	V42D	1.000
5:137940259:A:G	L905P	0.999
5:137940268:A:G	L902P	0.999
5:137940271:A:G	L901P	0.999
5:137940277:A:G	L899P	0.999
5:137940285:T:A	K896N	0.999
5:137940285:T:G	K896N	0.999
5:137940294:C:A	K893N	0.999

dbSNP variants (sampled 300 via entrez): RS1000008103 (5:138019541 T>C), RS1000018354 (5:137955068 A>G), RS1000023307 (5:138009069 G>A), RS1000035237 (5:138040749 G>T), RS1000079290 (5:137961674 T>C), RS1000085874 (5:138003139 C>G), RS1000102459 (5:138048595 G>A), RS1000161117 (5:137970119 G>T), RS1000175181 (5:137967885 C>A), RS1000251096 (5:138021359 G>A,T), RS1000305734 (5:138048135 G>T), RS1000331532 (5:138007283 T>C), RS1000334848 (5:137977623 T>A,C), RS1000337707 (5:138022996 T>C,G), RS1000367086 (5:137965903 T>C)

Disease associations

OMIM: gene MIM:609371 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST004297_4	Atrial fibrillation	1.000000e-08
GCST004521_66	Autism spectrum disorder or schizophrenia	1.000000e-08
GCST006061_108	Atrial fibrillation	2.000000e-32
GCST006414_139	Atrial fibrillation	1.000000e-35
GCST90002400_650	Plateletcrit	4.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007985	platelet crit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression, affects cotreatment, increases abundance	4
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases methylation	4
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
arsenite	affects binding, decreases reaction	1
cobaltous chloride	increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
Resveratrol	increases expression, affects cotreatment	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, affects cotreatment, decreases expression	1
Carbamazepine	affects expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Demecolcine	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Manganese	increases abundance, affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Niclosamide	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Quercetin	increases expression	1
Thiram	increases expression	1
Tunicamycin	increases expression	1
Vincristine	increases expression	1

Clinical trials (associated diseases)

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