FAM178B

Summary

FAM178B (family with sequence similarity 178 member B, HGNC:28036) is a protein-coding gene on chromosome 2q11.2, encoding Protein FAM178B (Q8IXR5).

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_001122646

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28036
Approved symbol	FAM178B
Name	family with sequence similarity 178 member B
Location	2q11.2
Locus type	gene with protein product
Status	Approved
Aliases	LOC51252
Ensembl gene	ENSG00000168754
Ensembl biotype	protein_coding
Entrez	51252

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding_CDS_not_defined, 2 protein_coding, 1 retained_intron

ENST00000393526, ENST00000470789, ENST00000478671, ENST00000490605, ENST00000494172, ENST00000520074

RefSeq mRNA: 3 — MANE Select: NM_001122646 NM_001122646, NM_001172667, NM_016490

CCDS: CCDS33252, CCDS46366

Canonical transcript exons

ENST00000490605 — 17 exons

Exon	Start	End
ENSE00001160740	96875885	96876308
ENSE00001625042	96902620	96902707
ENSE00001648149	96971901	96972322
ENSE00001649546	96970716	96970777
ENSE00001709577	96967520	96967627
ENSE00001760721	96960288	96960440
ENSE00001765239	96921478	96921654
ENSE00001784614	96921165	96921262
ENSE00001853587	96986241	96986580
ENSE00003473682	96947818	96947902
ENSE00003543521	96877890	96878042
ENSE00003564204	96878416	96878493
ENSE00003568560	96893926	96894051
ENSE00003581444	96972538	96972606
ENSE00003584816	96923490	96923583
ENSE00003596569	96929206	96929320
ENSE00003642817	96951379	96951484

Expression profiles

Bgee: expression breadth ubiquitous, 163 present calls, max score 89.35.

FANTOM5 (CAGE): breadth broad, TPM avg 0.9664 / max 52.4876, expressed in 213 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29787	0.3141	62
29788	0.2934	62
29790	0.1062	54
29789	0.0667	29
29814	0.0655	20
29797	0.0564	36
202306	0.0350	26
29815	0.0168	12
29813	0.0124	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	89.35	gold quality
spinal cord	UBERON:0002240	87.07	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.90	gold quality
left ventricle myocardium	UBERON:0006566	84.51	gold quality
cardiac muscle of right atrium	UBERON:0003379	84.44	gold quality
tibial nerve	UBERON:0001323	82.67	gold quality
kidney epithelium	UBERON:0004819	82.23	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.89	gold quality
superficial temporal artery	UBERON:0001614	81.25	gold quality
tibialis anterior	UBERON:0001385	80.34	silver quality
bone marrow	UBERON:0002371	79.57	gold quality
substantia nigra	UBERON:0002038	79.38	gold quality
upper arm skin	UBERON:0004263	78.09	gold quality
epithelium of nasopharynx	UBERON:0001951	77.91	gold quality
myocardium	UBERON:0002349	77.79	gold quality
bone marrow cell	CL:0002092	77.75	gold quality
midbrain	UBERON:0001891	77.71	gold quality
nasal cavity epithelium	UBERON:0005384	77.56	gold quality
putamen	UBERON:0001874	77.48	gold quality
sural nerve	UBERON:0015488	76.39	gold quality
cerebellar vermis	UBERON:0004720	75.64	gold quality
spleen	UBERON:0002106	75.38	gold quality
deltoid	UBERON:0001476	75.32	gold quality
prefrontal cortex	UBERON:0000451	75.28	gold quality
amygdala	UBERON:0001876	75.07	gold quality
Brodmann (1909) area 9	UBERON:0013540	74.92	gold quality
mucosa of paranasal sinus	UBERON:0005030	74.53	gold quality
left testis	UBERON:0004533	74.37	gold quality
right testis	UBERON:0004534	74.29	gold quality
quadriceps femoris	UBERON:0001377	74.23	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 12.

Experiment	Marker?	Max mean expression
E-MTAB-7407	yes	1568.28
E-CURD-98	yes	1262.16
E-CURD-112	yes	1136.47
E-MTAB-10042	yes	1019.41
E-ANND-5	yes	616.19
E-GEOD-130473	yes	521.74
E-MTAB-9067	yes	357.31
E-HCAD-4	yes	142.03
E-HCAD-8	yes	108.89
E-HCAD-6	yes	45.04
E-CURD-122	yes	22.80
E-ANND-3	yes	8.28
E-HCAD-10	no	1.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting FAM178B, 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-6825-5P	99.96	69.81	3431
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-3196	98.96	63.91	326
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-9500	98.62	66.54	1845
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-6816-5P	98.46	64.35	364
HSA-MIR-5008-5P	98.42	65.87	1019
HSA-MIR-484	98.16	66.92	1074
HSA-MIR-3155A	98.16	66.09	965
HSA-MIR-3155B	98.16	66.09	965
HSA-MIR-4649-5P	93.02	63.85	141
HSA-MIR-6729-5P	93.02	62.76	138
HSA-MIR-4508	90.37	59.62	240

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam178b	ENSMUSG00000046337
rattus_norvegicus	Fam178b	ENSRNOG00000023941

Paralogs (1): SLF2 (ENSG00000119906)

Protein

Protein identifiers

Protein FAM178B — Q8IXR5 (reviewed: Q8IXR5)

All UniProt accessions (1): Q8IXR5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM178 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8IXR5-3	3	yes
Q8IXR5-2	2
Q8IXR5-4	4

RefSeq proteins (3): NP_001116118, NP_001166138, NP_057574 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026161	FAM178	Family
IPR044276	CANIN_dom	Domain

Pfam: PF14816

UniProt features (9 total): splice variant 3, sequence conflict 2, chain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IXR5-F1	66.01	0.21

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, CAGCTG_AP4_Q5, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, AP1FJ_Q2, chr2q11, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, CHAF1B_TARGET_GENES, E2F5_TARGET_GENES, GREB1_TARGET_GENES, NFKBIA_TARGET_GENES, ZNF197_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

478 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM178B	FAHD2B	Q6P2I3	696
FAM178B	ITPRIPL1	Q6GPH6	593
FAM178B	ANKRD39	Q53RE8	590
FAM178B	ANKRD36	A6QL64	570
FAM178B	CNNM3	Q8NE01	541
FAM178B	LCA5L	O95447	531
FAM178B	CATSPERB	Q9H7T0	528
FAM178B	CCDC60	Q8IWA6	518
FAM178B	FER1L5	A0AVI2	506
FAM178B	ANKRD36C	Q5JPF3	480
FAM178B	ANKRD36B	Q8N2N9	461
FAM178B	LMAN2L	Q9H0V9	447
FAM178B	ZNF514	Q96K75	446
FAM178B	ASTL	Q6HA08	434
FAM178B	RBKS	Q9H477	425

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ZNF598	FAM178B	psi-mi:“MI:0915”(physical association)	0.000
LRSAM1	FAM178B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): FAM178B (Two-hybrid), FAM178B (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0JN53, A0PJX8, A1L1L2, A1L3T7, A4FV45, B0BMG8, E2JF22, G3HQ82, O15360, O43299, O70491, P60330, Q0KL00, Q0V8E7, Q17Q97, Q24JP3, Q3U829, Q49LS3, Q4QR83, Q562E7, Q5ND34, Q5R7B4, Q5T1A1, Q5XG04, Q6NUQ4, Q6PH58, Q6UX68, Q7L4E1, Q7Z412, Q8BGI5, Q8BM55, Q8BSD4, Q8BXV2, Q8C3R1, Q8C7B8, Q8IXR5, Q8K0R6, Q8N6S5, Q8R115, Q8VCA6

Diamond homologs: F1QB81, Q5REF4, Q6P9P0, Q8IX21, Q8IXR5, Q24JP3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

889 predictions. Top by Δscore:

Variant	Effect	Δscore
2:96878038:TCGCC:T	acceptor_gain	1.0000
2:96878039:CGCC:C	acceptor_gain	1.0000
2:96878039:CGCCC:C	acceptor_gain	1.0000
2:96878041:CC:C	acceptor_gain	1.0000
2:96878042:CC:C	acceptor_gain	1.0000
2:96878415:CCCA:C	donor_gain	1.0000
2:96876307:GCCTG:G	acceptor_loss	0.9900
2:96876309:C:CC	acceptor_gain	0.9900
2:96876309:CTG:C	acceptor_loss	0.9900
2:96876310:T:A	acceptor_loss	0.9900
2:96876315:C:CT	acceptor_gain	0.9900
2:96877884:CACCA:C	donor_loss	0.9900
2:96877885:ACCAC:A	donor_loss	0.9900
2:96877886:CCACC:C	donor_loss	0.9900
2:96877888:AC:A	donor_loss	0.9900
2:96877889:C:CT	donor_loss	0.9900
2:96877912:AGCT:A	donor_gain	0.9900
2:96877915:T:TA	donor_gain	0.9900
2:96877948:T:TA	donor_gain	0.9900
2:96878040:GCC:G	acceptor_gain	0.9900
2:96878041:CCCTG:C	acceptor_gain	0.9900
2:96878043:C:CC	acceptor_gain	0.9900
2:96878044:T:A	acceptor_loss	0.9900
2:96878045:G:C	acceptor_gain	0.9900
2:96878045:G:GC	acceptor_gain	0.9900
2:96878052:C:CT	acceptor_gain	0.9900
2:96878053:G:T	acceptor_gain	0.9900
2:96878408:AGACT:A	donor_loss	0.9900
2:96878409:GACT:G	donor_loss	0.9900
2:96878410:ACT:A	donor_loss	0.9900

AlphaMissense

4398 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:96877922:A:G	W659R	0.989
2:96877922:A:T	W659R	0.989
2:96902686:G:C	S528R	0.989
2:96902686:G:T	S528R	0.989
2:96902688:T:G	S528R	0.989
2:96960371:A:C	F268L	0.978
2:96960371:A:T	F268L	0.978
2:96960373:A:G	F268L	0.978
2:96878473:G:C	S599R	0.975
2:96878473:G:T	S599R	0.975
2:96878475:T:G	S599R	0.975
2:96921489:A:G	W485R	0.975
2:96921489:A:T	W485R	0.975
2:96951390:A:G	W328R	0.973
2:96951390:A:T	W328R	0.973
2:96921212:G:C	N505K	0.969
2:96921212:G:T	N505K	0.969
2:96877920:C:A	W659C	0.965
2:96877920:C:G	W659C	0.965
2:96960372:A:G	F268S	0.965
2:96960294:A:G	F294S	0.961
2:96921487:C:A	W485C	0.956
2:96921487:C:G	W485C	0.956
2:96972114:G:C	F117L	0.955
2:96972114:G:T	F117L	0.955
2:96972116:A:G	F117L	0.955
2:96877921:C:G	W659S	0.953
2:96929303:A:G	W366R	0.952
2:96929303:A:T	W366R	0.952
2:96947901:A:G	L332P	0.950

dbSNP variants (sampled 300 via entrez): RS1000061295 (2:96956929 C>A), RS1000077926 (2:96914127 G>A), RS1000131322 (2:96913962 A>C), RS1000153589 (2:96950476 G>A), RS1000188183 (2:96932416 A>G), RS1000214513 (2:96888445 G>A), RS1000231501 (2:96897011 C>A,T), RS1000258786 (2:96891066 A>C,G), RS1000336591 (2:96908988 C>A), RS1000337254 (2:96967206 A>C), RS1000353101 (2:96986606 C>A,T), RS1000354950 (2:96902350 C>T), RS1000355688 (2:96979923 T>C), RS1000384660 (2:96922164 G>C), RS1000395638 (2:96949187 A>AGT)

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

10 associations (top):

Study	Trait	p-value
GCST005081_1	Bipolar disorder lithium response (continuous) or schizophrenia	5.000000e-08
GCST008151_83	Waist circumference	4.000000e-07
GCST008160_116	Waist circumference	4.000000e-07
GCST010697_1	Cortical surface area (min-P)	6.000000e-12
GCST010698_17	Subcortical volume (min-P)	9.000000e-09
GCST010699_105	Brain morphology (min-P)	2.000000e-11
GCST010700_9	Cortical thickness (MOSTest)	9.000000e-14
GCST010701_54	Cortical surface area (MOSTest)	2.000000e-16
GCST010702_79	Subcortical volume (MOSTest)	5.000000e-09
GCST010703_322	Brain morphology (MOSTest)	1.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs6728642	Efficacy	3	lithium	Bipolar Disorder

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs6728642	FAM178B	3	0.00	1	lithium

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	2
FR900359	decreases phosphorylation	1
bisphenol A	affects cotreatment, increases methylation	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
2-palmitoylglycerol	increases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Arsenic	affects methylation	1
Folic Acid	decreases expression	1
Methapyrilene	increases methylation	1
Plant Extracts	decreases expression, affects cotreatment	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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