FAM124B

Summary

FAM124B (family with sequence similarity 124 member B, HGNC:26224) is a protein-coding gene on chromosome 2q36.2, encoding Protein FAM124B (Q9H5Z6).

Located in mitochondrion and nucleoplasm.

Source: NCBI Gene 79843 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 69 total
• MANE Select transcript: NM_001122779

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26224
Approved symbol	FAM124B
Name	family with sequence similarity 124 member B
Location	2q36.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22746
Ensembl gene	ENSG00000124019
Ensembl biotype	protein_coding
OMIM	618403
Entrez	79843

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000243806, ENST00000389874, ENST00000409685, ENST00000951903

RefSeq mRNA: 2 — MANE Select: NM_001122779 NM_001122779, NM_024785

CCDS: CCDS2461, CCDS46527

Canonical transcript exons

ENST00000409685 — 2 exons

Exon	Start	End
ENSE00001941742	224401037	224402107
ENSE00003515048	224378698	224380208

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 89.63.

FANTOM5 (CAGE): breadth broad, TPM avg 1.3054 / max 102.5033, expressed in 358 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
34234	0.7335	278
34236	0.4021	128
34233	0.1050	38
34235	0.0648	28

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.63	gold quality
placenta	UBERON:0001987	74.16	gold quality
superficial temporal artery	UBERON:0001614	72.52	gold quality
subcutaneous adipose tissue	UBERON:0002190	71.14	gold quality
monocyte	CL:0000576	69.24	gold quality
mononuclear cell	CL:0000842	69.06	gold quality
leukocyte	CL:0000738	68.99	gold quality
apex of heart	UBERON:0002098	67.90	gold quality
smooth muscle tissue	UBERON:0001135	67.52	gold quality
omental fat pad	UBERON:0010414	67.49	gold quality
peritoneum	UBERON:0002358	67.42	gold quality
adipose tissue	UBERON:0001013	67.34	gold quality
adipose tissue of abdominal region	UBERON:0007808	66.87	gold quality
connective tissue	UBERON:0002384	66.52	gold quality
colonic epithelium	UBERON:0000397	66.09	silver quality
lower lobe of lung	UBERON:0008949	65.60	silver quality
mucosa of paranasal sinus	UBERON:0005030	64.80	gold quality
visceral pleura	UBERON:0002401	63.75	gold quality
right lung	UBERON:0002167	63.68	gold quality
tibial nerve	UBERON:0001323	63.53	gold quality
heart left ventricle	UBERON:0002084	63.32	gold quality
upper lobe of lung	UBERON:0008948	63.22	gold quality
upper lobe of left lung	UBERON:0008952	62.97	gold quality
lower esophagus	UBERON:0013473	62.73	gold quality
lower esophagus muscularis layer	UBERON:0035833	62.71	gold quality
cardiac ventricle	UBERON:0002082	62.68	gold quality
calcaneal tendon	UBERON:0003701	62.63	gold quality
gastrocnemius	UBERON:0001388	62.48	gold quality
gall bladder	UBERON:0002110	62.27	gold quality
muscle of leg	UBERON:0001383	62.00	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-8271	yes	16.44
E-ANND-3	yes	5.23
E-MTAB-6678	no	2.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

86 targeting FAM124B, 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-9-5P	100.00	72.28	2361
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-1179	99.71	68.70	1040
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733
HSA-MIR-892C-3P	99.65	69.38	1745
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-1252-3P	99.55	67.71	2862

Literature-anchored findings (GeneRIF, showing 1)

• Fam124B is a novel protein possibly involved in the pathogenesis of CHARGE syndrome and neurodevelopmental disorders. (PMID:23285124)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam124b	ENSDARG00000087489
mus_musculus	Fam124b	ENSMUSG00000043230
rattus_norvegicus	Fam124b	ENSRNOG00000054416

Paralogs (1): FAM124A (ENSG00000150510)

Protein

Protein identifiers

Protein FAM124B — Q9H5Z6 (reviewed: Q9H5Z6)

All UniProt accessions (1): Q9H5Z6

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with CHD7 and CHD8.

Subcellular location. Nucleus.

Similarity. Belongs to the FAM124 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H5Z6-1	1	yes
Q9H5Z6-2	2

RefSeq proteins (2): NP_001116251, NP_079061 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029380	FAM124	Family
IPR046365	FAM124_dom	Domain

Pfam: PF15067

UniProt features (10 total): sequence conflict 3, splice variant 2, chain 1, region of interest 1, compositionally biased region 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H5Z6-F1	63.74	0.30

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 (1): 49

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9943962	CHD6, CHD7, CHD8, CHD9 subfamily

MSigDB gene sets: 78 (showing top): GGTGAAG_MIR412, HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP, CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN, IL15_UP.V1_DN, IL2_UP.V1_DN, IL21_UP.V1_DN, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_UP, LMTK3_TARGET_GENES, TFEB_TARGET_GENES, ZNF592_TARGET_GENES, ZNF766_TARGET_GENES, MIR548AA_MIR548AP_3P_MIR548T_3P, MIR186_5P, MIR497_3P, MIR4778_3P

GO Biological Process (0):

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

GO Cellular Component (3): nucleoplasm (GO:0005654), mitochondrion (GO:0005739), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
CHD chromatin remodelers	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	2
binding	1
nuclear lumen	1
cellular anatomical structure	1
cytoplasm	1

Protein interactions and networks

STRING

376 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM124B	CHD8	Q9HCK8	760
FAM124B	CHD7	Q9P2D1	571
FAM124B	FAM174B	Q3ZCQ3	518
FAM124B	OR2A2	Q6IF42	478
FAM124B	MANEAL	Q5VSG8	448
FAM124B	SPATA13	Q96N96	445
FAM124B	FAM167B	Q9BTA0	437
FAM124B	FAM124A	Q86V42	432
FAM124B	EBLN2	Q6P2I7	419
FAM124B	ZNF254	O75437	418
FAM124B	RCN2	Q14257	416
FAM124B	SPDYE3	A6NKU9	414
FAM124B	HPDL	Q96IR7	407
FAM124B	NAV1	Q8NEY1	404
FAM124B	RPP38	P78345	398

IntAct

87 interactions, top by confidence:

A	B	Type	Score
FAM124B	MDFI	psi-mi:“MI:0915”(physical association)	0.710
MDFI	FAM124B	psi-mi:“MI:0915”(physical association)	0.710
	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
KRT19	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
TCF4	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
FAM124B	KRTAP5-9	psi-mi:“MI:0915”(physical association)	0.560
FAM124B	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
FAM124B	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.560
FAM124B	TLE5	psi-mi:“MI:0915”(physical association)	0.560
FAM124B	GOLGA2	psi-mi:“MI:0915”(physical association)	0.560
MKRN3	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
FAM124B	KRT31	psi-mi:“MI:0915”(physical association)	0.560
KRT40	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
RINT1	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
ADAMTSL4	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
KCTD9	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
NOTCH2NLA	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
USHBP1	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
KIAA1958	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
FAM124B	KCTD6	psi-mi:“MI:0915”(physical association)	0.560
FAM124B	RBPMS	psi-mi:“MI:0915”(physical association)	0.560
BIRC7	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
FAM124B	LZTS2	psi-mi:“MI:0915”(physical association)	0.560
TRIM54	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
CARD9	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
SSX2IP	FAM124B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (78): FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), FAM124B (Two-hybrid), USHBP1 (Two-hybrid)

ESM2 similar proteins: A1L3T7, A2AKB4, A2RU30, A5GFW5, A6NP61, A6QLD5, A7E316, B1ASB6, P60924, Q08DK9, Q1XFL1, Q2TAK8, Q2YDQ5, Q3TD16, Q3TYX8, Q3U132, Q3U1D0, Q400C9, Q49AM3, Q571B6, Q5JXC2, Q5JYT7, Q5RA50, Q5SYB0, Q66IK8, Q6DIL6, Q6GQ34, Q6IRU7, Q6P1D7, Q6P1H6, Q6P4T1, Q7TNY7, Q7TSI1, Q7Z572, Q80XI1, Q86V42, Q8BG26, Q8BLQ0, Q8BP86, Q8BVF9

Diamond homologs: A6QLD5, Q5RA50, Q66IK8, Q6DIL6, Q6GQ34, Q86V42, Q8BLQ0, Q9H5Z6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 33 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	6	15.9×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

227 predictions. Top by Δscore:

Variant	Effect	Δscore
2:224380209:C:CA	acceptor_loss	0.9900
2:224380209:C:CC	acceptor_gain	0.9900
2:224401032:AATAC:A	donor_loss	0.9900
2:224401033:ATAC:A	donor_loss	0.9900
2:224401034:TAC:T	donor_loss	0.9900
2:224401035:AC:A	donor_loss	0.9900
2:224401036:C:A	donor_loss	0.9900
2:224380204:TGAAC:T	acceptor_gain	0.9800
2:224380205:GAAC:G	acceptor_gain	0.9800
2:224380213:A:T	acceptor_gain	0.9800
2:224380207:AC:A	acceptor_gain	0.9700
2:224380208:CC:C	acceptor_gain	0.9700
2:224380212:C:CT	acceptor_gain	0.9700
2:224401063:AGT:A	donor_gain	0.9600
2:224380206:AAC:A	acceptor_gain	0.9500
2:224401140:TGA:T	donor_gain	0.9500
2:224380205:GAACC:G	acceptor_gain	0.9400
2:224380207:ACCT:A	acceptor_gain	0.9400
2:224401037:C:G	donor_loss	0.9400
2:224380206:AACCT:A	acceptor_gain	0.9200
2:224380208:CCT:C	acceptor_gain	0.9200
2:224380209:C:G	acceptor_gain	0.9100
2:224380210:T:A	acceptor_gain	0.9100
2:224400424:TGA:T	donor_gain	0.9100
2:224401138:CTTGA:C	donor_gain	0.8800
2:224401074:TGC:T	donor_gain	0.8100
2:224401152:TGCAG:T	donor_gain	0.8100
2:224401126:A:AC	donor_gain	0.8000
2:224401127:C:CC	donor_gain	0.8000
2:224381987:CA:C	donor_gain	0.7800

AlphaMissense

2985 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:224401078:A:G	W231R	0.996
2:224401078:A:T	W231R	0.996
2:224401149:A:G	F207S	0.996
2:224401076:C:A	W231C	0.995
2:224401076:C:G	W231C	0.995
2:224401393:A:G	W126R	0.995
2:224401393:A:T	W126R	0.995
2:224401066:C:G	D235H	0.992
2:224401088:G:C	S227R	0.990
2:224401088:G:T	S227R	0.990
2:224401090:T:G	S227R	0.990
2:224401644:A:G	F42S	0.990
2:224401044:A:G	L242P	0.989
2:224401065:T:A	D235V	0.989
2:224401077:C:G	W231S	0.989
2:224401148:A:C	F207L	0.989
2:224401148:A:T	F207L	0.989
2:224401150:A:G	F207L	0.989
2:224401489:A:G	W94R	0.989
2:224401489:A:T	W94R	0.989
2:224401064:G:C	D235E	0.988
2:224401064:G:T	D235E	0.988
2:224401487:C:A	W94C	0.988
2:224401487:C:G	W94C	0.988
2:224401065:T:G	D235A	0.987
2:224401113:A:G	L219P	0.986
2:224401305:A:G	L155P	0.986
2:224401315:C:G	A152P	0.986
2:224401041:A:G	L243P	0.985
2:224401728:A:G	L14P	0.985

dbSNP variants (sampled 300 via entrez): RS1000206890 (2:224386226 G>A,T), RS1000364115 (2:224403965 AAC>A), RS1000451886 (2:224397761 T>C), RS1000568038 (2:224398030 T>A), RS1000648527 (2:224387404 C>G), RS1000669880 (2:224393682 G>C), RS1000928779 (2:224380778 C>A), RS1000941498 (2:224387646 C>T), RS1001065849 (2:224393453 G>A), RS1001139021 (2:224402890 C>A,T), RS1001233131 (2:224401341 T>TAC), RS1001504303 (2:224391576 T>G), RS1001556623 (2:224391933 C>T), RS1001836698 (2:224393061 A>G), RS1001951145 (2:224392721 C>A,T)

Disease associations

OMIM: gene MIM:618403 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST006088_63	Familial squamous cell lung carcinoma	8.000000e-06
GCST008521_11	Bitter beverage consumption	2.000000e-06
GCST008524_13	Bitter non-alcoholic beverage consumption	5.000000e-07

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006953	family history of lung cancer
EFO:0010089	bitter beverage consumption measurement
EFO:0010093	bitter non-alcoholic beverage consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
Air Pollutants	affects methylation, increases abundance	1
Benzo(a)pyrene	increases methylation, decreases methylation	1
Latex	increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Nitrogen Dioxide	affects methylation, increases abundance	1
Thimerosal	decreases expression	1
Aflatoxin B1	increases methylation	1
Asbestos, Serpentine	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	affects methylation, increases abundance	1

Clinical trials (associated diseases)

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