FAM78B

Summary

FAM78B (family with sequence similarity 78 member B, HGNC:13495) is a protein-coding gene on chromosome 1q24.1, encoding Protein FAM78B (Q5VT40).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 27 total
• MANE Select transcript: NM_001017961

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13495
Approved symbol	FAM78B
Name	family with sequence similarity 78 member B
Location	1q24.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000188859
Ensembl biotype	protein_coding
Entrez	149297

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 nonsense_mediated_decay, 2 protein_coding

ENST00000338353, ENST00000354422, ENST00000435676, ENST00000441649, ENST00000456900

RefSeq mRNA: 1 — MANE Select: NM_001017961 NM_001017961

CCDS: CCDS30931

Canonical transcript exons

ENST00000354422 — 2 exons

Exon	Start	End
ENSE00001369706	166165986	166167001
ENSE00001445843	166069299	166070763

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 88.62.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2816 / max 32.7399, expressed in 485 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15744	0.6344	304
15741	0.3729	159
15743	0.1657	83
15742	0.1085	52

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	88.62	gold quality
Brodmann (1909) area 23	UBERON:0013554	82.00	gold quality
cortical plate	UBERON:0005343	81.23	gold quality
primary visual cortex	UBERON:0002436	80.20	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.87	gold quality
middle temporal gyrus	UBERON:0002771	78.53	gold quality
occipital lobe	UBERON:0002021	77.81	gold quality
prefrontal cortex	UBERON:0000451	77.58	gold quality
right hemisphere of cerebellum	UBERON:0014890	77.43	gold quality
cerebellar cortex	UBERON:0002129	77.10	gold quality
cerebellar hemisphere	UBERON:0002245	77.09	gold quality
cerebellum	UBERON:0002037	76.62	gold quality
gastrocnemius	UBERON:0001388	76.24	gold quality
frontal cortex	UBERON:0001870	75.80	gold quality
neocortex	UBERON:0001950	75.61	gold quality
right frontal lobe	UBERON:0002810	75.46	gold quality
muscle of leg	UBERON:0001383	75.28	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	75.09	gold quality
Brodmann (1909) area 9	UBERON:0013540	74.69	gold quality
anterior cingulate cortex	UBERON:0009835	74.39	gold quality
cerebral cortex	UBERON:0000956	74.18	gold quality
superior frontal gyrus	UBERON:0002661	73.25	gold quality
cerebellar vermis	UBERON:0004720	73.21	silver quality
nucleus accumbens	UBERON:0001882	72.89	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	72.85	gold quality
hindlimb stylopod muscle	UBERON:0004252	72.84	gold quality
postcentral gyrus	UBERON:0002581	72.33	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.17	gold quality
parietal lobe	UBERON:0001872	71.91	gold quality
brain	UBERON:0000955	71.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting FAM78B, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-4658	99.77	64.94	514
HSA-MIR-6790-5P	99.77	65.24	505
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-182-3P	99.57	67.57	825
HSA-MIR-4284	99.36	65.25	1293
HSA-MIR-2116-5P	99.32	69.34	1273
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-331-3P	98.76	64.91	793
HSA-MIR-4520-3P	98.75	66.55	963
HSA-MIR-1537-5P	98.70	68.33	999
HSA-MIR-5094	98.63	67.11	1062
HSA-MIR-541-5P	98.24	67.77	1181
HSA-MIR-218-2-3P	98.08	67.21	601
HSA-MIR-6842-3P	98.07	66.33	1325

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam78ba	ENSDARG00000063018
danio_rerio	fam78bb	ENSDARG00000113552
mus_musculus	Fam78b	ENSMUSG00000060568
rattus_norvegicus	Fam78b	ENSRNOG00000068017

Paralogs (1): FAM78A (ENSG00000126882)

Protein

Protein identifiers

Protein FAM78B — Q5VT40 (reviewed: Q5VT40)

All UniProt accessions (3): H7C075, H7C3M6, Q5VT40

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM78 family.

RefSeq proteins (1): NP_001017961* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029638	FAM78	Family

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VT40-F1	95.02	0.93

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): CCAGGGG_MIR331, CTGAGCC_MIR24, TTTGCAG_MIR518A2, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_UP, CTTTGCA_MIR527, GSE13522_WT_VS_IFNAR_KO_SKIN_UP, GSE13547_WT_VS_ZFX_KO_BCELL_UP, ZNF407_TARGET_GENES, MIR8485, MIR6867_5P, MIR506_3P, MIR124_3P, MIR4762_3P, MIR765, MIR6756_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

380 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM78B	C12orf43	Q96C57	550
FAM78B	ALPK1	Q96QP1	370
FAM78B	C1orf198	Q9H425	365
FAM78B	ECT2L	Q008S8	364
FAM78B	TMC7	Q7Z402	354
FAM78B	CPNE8	Q86YQ8	352
FAM78B	MEX3A	A1L020	346
FAM78B	ACTBL2	Q562R1	346
FAM78B	CIAO2B	Q9Y3D0	324
FAM78B	TRABD2A	Q86V40	314
FAM78B	PAPLN	O95428	312
FAM78B	XXYLT1	Q8NBI6	305
FAM78B	UMODL1	Q5DID0	304
FAM78B	SPPL2B	Q8TCT7	304
FAM78B	GXYLT2	A0PJZ3	303

IntAct

4 interactions, top by confidence:

A	B	Type	Score
FAM78B	RPS27A	psi-mi:“MI:0914”(association)	0.530
FAM78B	FRYL	psi-mi:“MI:0914”(association)	0.350
	SHTN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): RPS27A (Affinity Capture-MS), MAD2L2 (Affinity Capture-MS), ANKRD13D (Affinity Capture-MS), VPS13C (Affinity Capture-MS), FRYL (Affinity Capture-MS), ANKRD13D (Affinity Capture-MS), MAD2L2 (Affinity Capture-MS), VPS13C (Affinity Capture-MS), RPS27A (Affinity Capture-MS)

ESM2 similar proteins: A1XFV8, A3RM21, A7WNB1, A7YWU3, A8C8K0, B2ZCQ0, B2ZCQ1, B2ZCQ2, B2ZCQ3, C6EN00, F5HDY6, F5HGN8, O36412, O92277, P07051, P09280, P0C338, P0C339, P0C340, P0CF75, P12792, P13140, P15397, P16628, P20403, P21406, P22046, P27557, P28935, P28954, P31611, P36714, P84406, P9WEK0, Q00147, Q00151, Q04350, Q07FH9, Q0GBY2, Q197F9

Diamond homologs: Q5JUQ0, Q5VT40, Q8BQN5, Q8C552

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1374 predictions. Top by Δscore:

Variant	Effect	Δscore
1:166070781:A:C	acceptor_gain	1.0000
1:166165985:CATG:C	donor_gain	1.0000
1:166140942:A:AC	donor_gain	0.9900
1:166140943:C:CC	donor_gain	0.9900
1:166165984:A:AC	donor_gain	0.9900
1:166165984:ACATG:A	donor_gain	0.9900
1:166165985:C:CC	donor_gain	0.9900
1:166165985:CATGC:C	donor_gain	0.9900
1:166165988:G:A	donor_gain	0.9900
1:166070764:CT:C	acceptor_loss	0.9800
1:166070765:T:A	acceptor_loss	0.9800
1:166070768:C:CT	acceptor_gain	0.9800
1:166070773:C:CT	acceptor_gain	0.9800
1:166071106:T:A	donor_gain	0.9800
1:166130374:C:CT	acceptor_gain	0.9800
1:166165039:AG:A	donor_gain	0.9800
1:166070764:C:CC	acceptor_gain	0.9700
1:166070784:C:CT	acceptor_gain	0.9700
1:166130365:C:CC	acceptor_gain	0.9700
1:166130375:A:T	acceptor_gain	0.9700
1:166166083:C:CT	donor_gain	0.9700
1:166070774:A:T	acceptor_gain	0.9600
1:166070781:A:AC	acceptor_gain	0.9600
1:166070769:A:T	acceptor_gain	0.9500
1:166070780:CA:C	acceptor_gain	0.9500
1:166070759:TTGAC:T	acceptor_gain	0.9400
1:166165980:GCTT:G	donor_loss	0.9400
1:166165981:CTTA:C	donor_loss	0.9400
1:166165982:TTA:T	donor_loss	0.9400
1:166165983:TACA:T	donor_loss	0.9400

AlphaMissense

1719 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:166070286:C:A	W247C	1.000
1:166070286:C:G	W247C	1.000
1:166070287:C:G	W247S	1.000
1:166070288:A:G	W247R	1.000
1:166070288:A:T	W247R	1.000
1:166070293:A:G	L245P	1.000
1:166070293:A:T	L245H	1.000
1:166070298:C:A	Q243H	1.000
1:166070298:C:G	Q243H	1.000
1:166070303:C:G	A242P	1.000
1:166070307:A:C	N240K	1.000
1:166070307:A:T	N240K	1.000
1:166070309:T:C	N240D	1.000
1:166070311:G:T	A239D	1.000
1:166070317:G:T	P237H	1.000
1:166070318:G:A	P237S	1.000
1:166070368:G:C	P220R	1.000
1:166070368:G:T	P220H	1.000
1:166070369:G:A	P220S	1.000
1:166070401:G:T	A209D	1.000
1:166070437:A:T	I197N	1.000
1:166070454:C:A	W191C	1.000
1:166070454:C:G	W191C	1.000
1:166070455:C:G	W191S	1.000
1:166070456:A:G	W191R	1.000
1:166070456:A:T	W191R	1.000
1:166070470:A:G	L186P	1.000
1:166070503:G:T	A175D	1.000
1:166070509:A:G	L173P	1.000
1:166070509:A:T	L173Q	1.000

dbSNP variants (sampled 300 via entrez): RS1000006492 (1:166162344 T>C), RS1000015354 (1:166107824 C>G), RS1000106707 (1:166167569 A>C,G), RS1000111359 (1:166130272 G>A), RS1000147020 (1:166113079 T>C), RS1000147211 (1:166082153 A>T), RS1000204471 (1:166101946 G>C), RS1000218869 (1:166131583 AG>A,AGGGG), RS1000268692 (1:166130114 C>T), RS1000281860 (1:166134445 C>G,T), RS1000311921 (1:166088219 A>C), RS1000356422 (1:166162679 T>A), RS1000362894 (1:166099704 C>A,T), RS1000386981 (1:166096839 G>T), RS1000445243 (1:166090804 C>CTGA)

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
GCST007325_210	General risk tolerance (MTAG)	2.000000e-08
GCST012225_1	Cocaine dependence (time to event)	4.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008579	risk-taking behaviour

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
Benzo(a)pyrene	decreases expression, decreases methylation	2
methyleugenol	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
arsenite	increases methylation	1
sodium arsenite	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	decreases expression	1
Cisplatin	decreases expression	1
Nickel	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Thiram	decreases expression	1
Tretinoin	increases expression	1
Triclosan	increases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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