FAM219B

Summary

FAM219B (family with sequence similarity 219 member B, HGNC:24695) is a protein-coding gene on chromosome 15q24.1-q24.2, encoding Protein FAM219B (Q5XKK7).

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_020447

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24695
Approved symbol	FAM219B
Name	family with sequence similarity 219 member B
Location	15q24.1-q24.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ00005
Ensembl gene	ENSG00000178761
Ensembl biotype	protein_coding
Entrez	57184

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 11 nonsense_mediated_decay, 7 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000357635, ENST00000562698, ENST00000563069, ENST00000563119, ENST00000563413, ENST00000563671, ENST00000563706, ENST00000563877, ENST00000564019, ENST00000564723, ENST00000564857, ENST00000565772, ENST00000566132, ENST00000566194, ENST00000566894, ENST00000567388, ENST00000569524, ENST00000569761, ENST00000570143, ENST00000878718, ENST00000878719, ENST00000937931

RefSeq mRNA: 5 — MANE Select: NM_020447 NM_001321920, NM_001321921, NM_001321922, NM_001321923, NM_020447

CCDS: CCDS32295

Canonical transcript exons

ENST00000357635 — 5 exons

Exon	Start	End
ENSE00001296950	74906587	74906851
ENSE00002603955	74899992	74902786
ENSE00003573282	74904664	74904712
ENSE00003573380	74906278	74906365
ENSE00003633944	74905154	74905231

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 97.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.9647 / max 185.3499, expressed in 1796 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
150938	7.2244	1770
150939	2.3971	1319
150940	0.7526	296
150937	0.5016	151
150936	0.0891	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	97.90	gold quality
cardiac muscle of right atrium	UBERON:0003379	97.09	gold quality
upper arm skin	UBERON:0004263	96.92	gold quality
lower esophagus mucosa	UBERON:0035834	95.99	gold quality
left ventricle myocardium	UBERON:0006566	95.91	gold quality
adenohypophysis	UBERON:0002196	95.87	gold quality
apex of heart	UBERON:0002098	95.83	gold quality
pituitary gland	UBERON:0000007	95.82	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.78	gold quality
cerebellar hemisphere	UBERON:0002245	95.73	gold quality
cerebellar cortex	UBERON:0002129	95.72	gold quality
primary visual cortex	UBERON:0002436	95.64	gold quality
cerebellum	UBERON:0002037	95.49	gold quality
Brodmann (1909) area 23	UBERON:0013554	95.21	gold quality
cardiac atrium	UBERON:0002081	95.08	gold quality
lower esophagus	UBERON:0013473	95.07	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.07	gold quality
right atrium auricular region	UBERON:0006631	94.98	gold quality
endothelial cell	CL:0000115	94.93	gold quality
middle temporal gyrus	UBERON:0002771	94.89	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.87	gold quality
esophagus	UBERON:0001043	94.83	gold quality
myocardium	UBERON:0002349	94.81	gold quality
esophagus mucosa	UBERON:0002469	94.71	gold quality
occipital lobe	UBERON:0002021	94.56	gold quality
ascending aorta	UBERON:0001496	94.50	gold quality
thoracic aorta	UBERON:0001515	94.50	gold quality
heart left ventricle	UBERON:0002084	94.50	gold quality
right coronary artery	UBERON:0001625	94.45	gold quality
cardiac ventricle	UBERON:0002082	94.44	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

87 targeting FAM219B, 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-3120-5P	100.00	65.56	965
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687
HSA-MIR-520B-3P	99.83	70.56	1699
HSA-MIR-520C-3P	99.83	70.56	1699

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam219b	ENSDARG00000104637
mus_musculus	Fam219b	ENSMUSG00000032305
rattus_norvegicus	Fam219b	ENSRNOG00000054468

Paralogs (1): FAM219A (ENSG00000164970)

Protein

Protein identifiers

Protein FAM219B — Q5XKK7 (reviewed: Q5XKK7)

All UniProt accessions (9): Q5XKK7, A0A0G2JLB0, H3BM86, H3BMU7, H3BMY2, H3BNG0, H3BPC2, H3BRU1, H3BSK2

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM219 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5XKK7-1	1	yes
Q5XKK7-2	2
Q5XKK7-3	3

RefSeq proteins (5): NP_001308849, NP_001308850, NP_001308851, NP_001308852, NP_065180* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029339	FAM219	Family

Pfam: PF15260

UniProt features (12 total): splice variant 4, modified residue 4, region of interest 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5XKK7-F1	66.08	0.06

Functional residue map

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

Post-translational modifications (4): 14, 91, 125, 127

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 80 (showing top): FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, LU_EZH2_TARGETS_UP, ZWANG_DOWN_BY_2ND_EGF_PULSE, DLX6_TARGET_GENES, HES2_TARGET_GENES, GSE10240_CTRL_VS_IL22_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_DN, MIR106B_5P, MIR20A_5P, MIR106A_5P, MIR17_5P, MIR20B_5P, MIR93_5P

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

332 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM219B	PRMT2IP	Q6ZRI6	581
FAM219B	SCAMP2	O15127	506
FAM219B	FAM221A	A4D161	479
FAM219B	ULK3	Q6PHR2	476
FAM219B	BSDC1	Q9NW68	451
FAM219B	ANKS1A	Q92625	451
FAM219B	LMAN1L	Q9HAT1	447
FAM219B	PGCKA1	Q8IY42	432
FAM219B	CCDC69	A6NI79	428
FAM219B	BLTP3A	Q6BDS2	422
FAM219B	KATNBL1	Q9H079	398
FAM219B	RPP25	Q9BUL9	396
FAM219B	GOLGA6A	Q9NYA3	393
FAM219B	ZNF254	O75437	380
FAM219B	FBXO41	Q8TF61	376

IntAct

18 interactions, top by confidence:

A	B	Type	Score
FAM219B	MEOX2	psi-mi:“MI:0915”(physical association)	0.560
FAM219B	PICK1	psi-mi:“MI:0915”(physical association)	0.560
FAM219B	AP1M1	psi-mi:“MI:0915”(physical association)	0.560
HOXA1	FAM219B	psi-mi:“MI:0915”(physical association)	0.560
FAM219B	SPAG9	psi-mi:“MI:0914”(association)	0.350
SLC1A3	DDX11L8	psi-mi:“MI:0914”(association)	0.350
FHIP2A	MED19	psi-mi:“MI:2364”(proximity)	0.270
FAM219B	MEOX2	psi-mi:“MI:0915”(physical association)	0.000
FAM219B	PICK1	psi-mi:“MI:0915”(physical association)	0.000
AP1M1	FAM219B	psi-mi:“MI:0915”(physical association)	0.000
FAM219B	HOXA1	psi-mi:“MI:0915”(physical association)	0.000
PICK1	FAM219B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (37): SPAG9 (Affinity Capture-MS), IKBKAP (Affinity Capture-MS), DPH2 (Affinity Capture-MS), ELP2 (Affinity Capture-MS), MTCH2 (Affinity Capture-MS), TRMU (Affinity Capture-MS), ELP3 (Affinity Capture-MS), TRMU (Affinity Capture-MS), DPH2 (Affinity Capture-MS), ELP3 (Affinity Capture-MS), SPAG9 (Affinity Capture-MS), MTCH2 (Affinity Capture-MS), ELP2 (Affinity Capture-MS), FAM219B (Two-hybrid), FAM219B (Two-hybrid)

ESM2 similar proteins: A0A088MLT8, A2AQ25, B3KU38, B5DF41, E9PSK7, O15079, O35274, P0DPB3, P0DPB4, P12755, P49140, P85299, Q0D2I5, Q14DQ1, Q1LY51, Q3B7M3, Q3SYW5, Q4KMA0, Q4R3X1, Q50H33, Q5F3L9, Q5FVG6, Q5RD40, Q5XKK7, Q60698, Q6ZNC4, Q6ZUS6, Q6ZWB6, Q80U23, Q80U62, Q80XA6, Q812A5, Q86YI8, Q8BXL9, Q8K2W6, Q8ND83, Q8NFH8, Q8QFX1, Q8TEK3, Q924W7

Diamond homologs: Q14DQ1, Q5XKK7, Q6DC60, Q8IW50, Q9BGQ5, Q9D772

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1416 predictions. Top by Δscore:

Variant	Effect	Δscore
15:74902787:C:CC	acceptor_gain	1.0000
15:74905149:CTCA:C	donor_loss	1.0000
15:74905150:TCAC:T	donor_loss	1.0000
15:74905151:CA:C	donor_loss	1.0000
15:74905152:ACCT:A	donor_loss	1.0000
15:74905229:GACCT:G	acceptor_loss	1.0000
15:74906283:C:A	donor_gain	1.0000
15:74906585:A:AC	donor_gain	1.0000
15:74906586:C:CC	donor_gain	1.0000
15:74906586:CG:C	donor_gain	1.0000
15:74902783:CCTG:C	acceptor_loss	0.9900
15:74902784:CTG:C	acceptor_gain	0.9900
15:74902785:TG:T	acceptor_gain	0.9900
15:74902785:TGCTA:T	acceptor_loss	0.9900
15:74902786:GC:G	acceptor_loss	0.9900
15:74902787:CTA:C	acceptor_loss	0.9900
15:74902788:T:A	acceptor_loss	0.9900
15:74905152:A:AC	donor_gain	0.9900
15:74905153:C:CC	donor_gain	0.9900
15:74905227:CTGAC:C	acceptor_gain	0.9900
15:74905232:C:CC	acceptor_gain	0.9900
15:74906217:T:TA	donor_gain	0.9900
15:74906228:AAAG:A	donor_gain	0.9900
15:74906586:CGCAG:C	donor_gain	0.9900
15:74902779:TTCAC:T	acceptor_gain	0.9800
15:74902780:TCAC:T	acceptor_gain	0.9800
15:74902781:CACC:C	acceptor_gain	0.9800
15:74906194:TAA:T	donor_gain	0.9800
15:74906195:AAA:A	donor_gain	0.9800
15:74906579:ACACT:A	donor_loss	0.9800

AlphaMissense

1259 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:74902710:A:G	L169S	0.991
15:74902704:A:G	L171P	0.990
15:74902744:A:C	Y158D	0.988
15:74902701:A:G	I172T	0.986
15:74902758:A:G	L153P	0.986
15:74902743:T:G	Y158S	0.981
15:74902704:A:T	L171H	0.978
15:74902747:C:A	G157W	0.978
15:74902746:C:A	G157V	0.977
15:74902758:A:T	L153Q	0.974
15:74902744:A:G	Y158H	0.972
15:74905219:A:C	F105L	0.972
15:74905219:A:T	F105L	0.972
15:74905221:A:G	F105L	0.972
15:74902749:T:A	D156V	0.971
15:74902701:A:C	I172S	0.970
15:74902744:A:T	Y158N	0.969
15:74902746:C:T	G157E	0.969
15:74902734:T:A	D161V	0.968
15:74902701:A:T	I172N	0.966
15:74902706:G:C	D170E	0.963
15:74902706:G:T	D170E	0.963
15:74902707:T:A	D170V	0.960
15:74902708:C:G	D170H	0.956
15:74902710:A:C	L169W	0.956
15:74902737:A:G	L160P	0.954
15:74902707:T:C	D170G	0.953
15:74902735:C:G	D161H	0.951
15:74902737:A:T	L160Q	0.950
15:74902723:C:G	D165H	0.949

dbSNP variants (sampled 300 via entrez): RS1000271905 (15:74902662 CAGCAGG>C), RS1000281225 (15:74904146 G>A), RS1000302948 (15:74903127 CTGA>C), RS1000432880 (15:74908501 G>A), RS1000961058 (15:74898246 A>G), RS1001715109 (15:74901620 G>A), RS1001842641 (15:74906980 G>A), RS1002427854 (15:74905914 C>G), RS1002640680 (15:74902318 G>A,C), RS1002704783 (15:74899862 C>G), RS1002733968 (15:74901965 A>C), RS1002894217 (15:74908131 T>C), RS1003252552 (15:74908392 G>A), RS1003638039 (15:74906912 C>A,G,T), RS1003857626 (15:74898630 C>G,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:602579

GenCC curated gene-disease

Mondo (1): MPI-congenital disorder of glycosylation (MONDO:0011257)

Orphanet (1): MPI-CDG (Orphanet:79319)

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST004625_153	Monocyte count	4.000000e-10
GCST009685_46	Hypertension	6.000000e-10
GCST010796_5099	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-09
GCST010796_5100	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-09
GCST90002390_422	Mean corpuscular hemoglobin	8.000000e-13
GCST90002393_256	Monocyte count	5.000000e-18

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005091	monocyte count
EFO:0004327	electrocardiography
EFO:0004527	mean corpuscular hemoglobin

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C535740	Congenital disorder of glycosylation type 1B (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	6
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
butyraldehyde	decreases expression	1
coumarin	decreases phosphorylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression	1
NSC 689534	affects binding, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, increases expression	1
Caffeine	increases phosphorylation	1
Copper	affects binding, increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Nickel	decreases expression	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	increases expression, increases abundance	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03404869	PHASE1/PHASE2	UNKNOWN	Study of ORL-1M (D-mannose) in Patients With CDG-Ib
NCT03655223	Not specified	ENROLLING_BY_INVITATION	Early Check: Expanded Screening in Newborns