FAM124A

Summary

FAM124A (family with sequence similarity 124 member A, HGNC:26413) is a protein-coding gene on chromosome 13q14.3, encoding Protein FAM124A (Q86V42).

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 101 total
• MANE Select transcript: NM_001242312

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26413
Approved symbol	FAM124A
Name	family with sequence similarity 124 member A
Location	13q14.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ30707
Ensembl gene	ENSG00000150510
Ensembl biotype	protein_coding
Entrez	220108

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000280057, ENST00000322475, ENST00000497449, ENST00000615498

RefSeq mRNA: 3 — MANE Select: NM_001242312 NM_001242312, NM_001330522, NM_145019

CCDS: CCDS55900, CCDS81767, CCDS9427

Canonical transcript exons

ENST00000322475 — 4 exons

Exon	Start	End
ENSE00001380721	51280450	51284239
ENSE00001652453	51251468	51252201
ENSE00001789102	51231348	51231379
ENSE00001903124	51222398	51222569

Expression profiles

Bgee: expression breadth ubiquitous, 205 present calls, max score 94.16.

FANTOM5 (CAGE): breadth broad, TPM avg 4.4080 / max 271.8255, expressed in 780 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
135187	2.4498	677
135188	1.9582	427

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
inferior vagus X ganglion	UBERON:0005363	94.16	gold quality
corpus callosum	UBERON:0002336	93.93	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.07	gold quality
spinal cord	UBERON:0002240	90.79	gold quality
subthalamic nucleus	UBERON:0001906	89.93	gold quality
medulla oblongata	UBERON:0001896	87.75	gold quality
cortical plate	UBERON:0005343	87.05	gold quality
buccal mucosa cell	CL:0002336	86.73	gold quality
midbrain	UBERON:0001891	85.88	gold quality
superior vestibular nucleus	UBERON:0007227	85.87	gold quality
substantia nigra	UBERON:0002038	85.80	gold quality
dorsal plus ventral thalamus	UBERON:0001897	85.49	gold quality
lateral globus pallidus	UBERON:0002476	84.97	gold quality
ventral tegmental area	UBERON:0002691	84.76	gold quality
globus pallidus	UBERON:0001875	84.53	gold quality
kidney epithelium	UBERON:0004819	84.15	silver quality
substantia nigra pars reticulata	UBERON:0001966	84.05	gold quality
medial globus pallidus	UBERON:0002477	83.71	gold quality
pons	UBERON:0000988	83.61	gold quality
Ammon’s horn	UBERON:0001954	82.55	gold quality
lower esophagus muscularis layer	UBERON:0035833	82.55	gold quality
lower esophagus	UBERON:0013473	82.49	gold quality
ventricular zone	UBERON:0003053	81.73	gold quality
occipital lobe	UBERON:0002021	81.14	gold quality
Brodmann (1909) area 46	UBERON:0006483	81.13	gold quality
pigmented layer of retina	UBERON:0001782	81.08	gold quality
retina	UBERON:0000966	81.06	gold quality
primary visual cortex	UBERON:0002436	81.04	gold quality
left ventricle myocardium	UBERON:0006566	80.95	gold quality
substantia nigra pars compacta	UBERON:0001965	80.76	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

116 targeting FAM124A, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-3659	99.70	67.97	694
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-7157-5P	99.66	69.33	1829

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam124a	ENSMUSG00000035184
rattus_norvegicus	Fam124a	ENSRNOG00000009802

Paralogs (1): FAM124B (ENSG00000124019)

Protein

Protein identifiers

Protein FAM124A — Q86V42 (reviewed: Q86V42)

All UniProt accessions (1): Q86V42

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM124 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q86V42-1	1	yes
Q86V42-2	2
Q86V42-3	3

RefSeq proteins (3): NP_001229241, NP_001317451, NP_659456 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029380	FAM124	Family
IPR046365	FAM124_dom	Domain

Pfam: PF15067

UniProt features (15 total): compositionally biased region 5, region of interest 3, splice variant 3, sequence conflict 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86V42-F1	63.48	0.31

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 40 (showing top): TGCTGAY_UNKNOWN, COATES_MACROPHAGE_M1_VS_M2_UP, chr13q14, HOELZEL_NF1_TARGETS_DN, LEE_BMP2_TARGETS_UP, ZNF2_TARGET_GENES, MIR607, MIR3671, MIR3680_3P, MIR561_3P, MIR587, MIR1285_3P, MIR5189_5P, MIR520A_5P, MIR4653_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

450 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM124A	FAM167B	Q9BTA0	566
FAM124A	WDR49	Q8IV35	513
FAM124A	FHIP2A	Q5W0V3	485
FAM124A	SPACA9	Q96E40	482
FAM124A	TMIGD3	P0DMS9	470
FAM124A	ANKRD29	Q8N6D5	447
FAM124A	PDLIM3	Q53GG5	445
FAM124A	C19orf47	Q8N9M1	433
FAM124A	ZNF414	Q96IQ9	433
FAM124A	FAM124B	Q9H5Z6	432
FAM124A	SERPINE3	A8MV23	423
FAM124A	TEX261	Q6UWH6	419
FAM124A	GTF3C5	Q9Y5Q8	415
FAM124A	RNF122	Q9H9V4	406
FAM124A	INSYN2B	A6NMK8	400

IntAct

95 interactions, top by confidence:

A	B	Type	Score
FAM124A	PRKG1	psi-mi:“MI:0915”(physical association)	0.670
PRKG1	FAM124A	psi-mi:“MI:0915”(physical association)	0.670
FAM124A	SAXO1	psi-mi:“MI:0915”(physical association)	0.560
	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	FOXP2	psi-mi:“MI:0915”(physical association)	0.560
ZNF250	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
TLE5	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	ROCK1	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	ZNF165	psi-mi:“MI:0915”(physical association)	0.560
PHC2	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	IHO1	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	ZZZ3	psi-mi:“MI:0915”(physical association)	0.560
INO80E	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
ZBTB44	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	DOCK8	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	CEP70	psi-mi:“MI:0915”(physical association)	0.560
LNX1	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	STAC3	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	RAB3IP	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	KIFC3	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	TRIM54	psi-mi:“MI:0915”(physical association)	0.560
ZFP64	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
THAP1	FAM124A	psi-mi:“MI:0915”(physical association)	0.560
FAM124A	CGGBP1	psi-mi:“MI:0915”(physical association)	0.560
SAXO1	FAM124A	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (51): FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid), FAM124A (Two-hybrid)

ESM2 similar proteins: A2A8U2, A4D2P6, A4IG66, A7MCY6, B5DF41, D4AE48, O15079, O75129, O97676, P12755, P36956, P53349, P56720, P85299, Q0QWG9, Q1JPG0, Q3B7M3, Q3MHU5, Q3TPJ7, Q3U0L2, Q504T8, Q50H33, Q5FVG6, Q5SNT2, Q60416, Q60698, Q66K64, Q6DVA0, Q6NS60, Q6NS82, Q6ZWB6, Q7L4E1, Q80U23, Q80U62, Q80Z10, Q812A5, Q86V42, Q86XL3, Q8C0R7, Q8CC12

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	88
Likely benign	5
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

996 predictions. Top by Δscore:

Variant	Effect	Δscore
13:51222565:GGAGG:G	donor_gain	1.0000
13:51222566:GAGG:G	donor_gain	1.0000
13:51222566:GAGGG:G	donor_gain	1.0000
13:51222567:AGGG:A	donor_loss	1.0000
13:51222568:GG:G	donor_gain	1.0000
13:51222568:GGGT:G	donor_loss	1.0000
13:51222569:GG:G	donor_gain	1.0000
13:51222569:GGTG:G	donor_loss	1.0000
13:51222570:G:GG	donor_gain	1.0000
13:51222571:T:A	donor_loss	1.0000
13:51251457:C:CA	acceptor_gain	1.0000
13:51222567:A:T	donor_gain	0.9900
13:51231380:G:GG	donor_gain	0.9900
13:51251462:CCCCA:C	acceptor_loss	0.9900
13:51251464:CCAG:C	acceptor_loss	0.9900
13:51251465:CA:C	acceptor_loss	0.9900
13:51251466:A:AT	acceptor_loss	0.9900
13:51251467:G:A	acceptor_loss	0.9900
13:51280445:CACA:C	acceptor_loss	0.9900
13:51280447:CA:C	acceptor_loss	0.9900
13:51280448:A:AG	acceptor_gain	0.9900
13:51280448:A:C	acceptor_loss	0.9900
13:51280448:AG:A	acceptor_gain	0.9900
13:51280449:G:GG	acceptor_gain	0.9900
13:51280449:GG:G	acceptor_gain	0.9900
13:51231334:GTCTT:G	acceptor_loss	0.9800
13:51231339:GTGTT:G	acceptor_loss	0.9800
13:51231340:TGTTT:T	acceptor_loss	0.9800
13:51231341:GTTTC:G	acceptor_loss	0.9800
13:51231342:TTTCA:T	acceptor_loss	0.9800

AlphaMissense

3560 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:51251845:T:A	W160R	0.999
13:51251845:T:C	W160R	0.999
13:51252160:T:A	W265R	0.999
13:51252160:T:C	W265R	0.999
13:51251683:T:C	F106L	0.998
13:51251685:C:A	F106L	0.998
13:51251685:C:G	F106L	0.998
13:51251749:T:A	W128R	0.998
13:51251749:T:C	W128R	0.998
13:51252026:T:C	F220S	0.998
13:51252036:A:C	K223N	0.998
13:51252036:A:T	K223N	0.998
13:51251751:G:C	W128C	0.997
13:51251751:G:T	W128C	0.997
13:51251848:G:C	A161P	0.997
13:51252162:G:C	W265C	0.997
13:51252162:G:T	W265C	0.997
13:51251603:T:C	F79S	0.996
13:51251684:T:C	F106S	0.996
13:51252089:T:C	F241S	0.996
13:51252194:T:C	L276P	0.996
13:51251507:T:A	V47D	0.995
13:51251885:G:C	R173P	0.995
13:51251888:T:C	F174S	0.995
13:51252035:A:T	K223I	0.995
13:51252172:G:C	D269H	0.995
13:51252173:A:T	D269V	0.995
13:51252197:T:C	L277P	0.995
13:51251515:C:G	H50D	0.994
13:51251671:G:C	A102P	0.994

dbSNP variants (sampled 300 via entrez): RS1000043224 (13:51227988 A>G), RS1000083001 (13:51246408 G>A,C,T), RS1000143233 (13:51272928 G>A), RS1000160926 (13:51241302 G>A), RS1000225685 (13:51259164 C>A), RS1000249198 (13:51279637 C>T), RS1000254609 (13:51258952 G>A), RS1000270878 (13:51234766 T>A,C), RS1000341120 (13:51247258 A>G), RS1000384597 (13:51265553 A>C), RS1000438471 (13:51265986 C>G), RS1000445776 (13:51220815 T>C), RS1000465866 (13:51254111 G>A), RS1000604545 (13:51254636 T>C), RS1000643148 (13:51257738 G>A)

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

7 associations (top):

Study	Trait	p-value
GCST002357_3	Rheumatoid arthritis (ACPA-negative)	1.000000e-06
GCST003134_14	Cerebrospinal fluid clusterin levels	5.000000e-06
GCST005844_1	Placental abruption	9.000000e-06
GCST007052_10	Lipoprotein (a) levels	5.000000e-07
GCST009391_1303	Metabolite levels	1.000000e-06
GCST010002_187	Refractive error	9.000000e-09
GCST012485_10	Cerebral amyloid angiopathy x sex interaction in Alzheimer’s disease	7.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006925	lipoprotein A measurement
EFO:0010517	oxalate measurement
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases expression	6
trichostatin A	affects cotreatment, decreases expression, increases expression	3
Benzo(a)pyrene	decreases expression, decreases methylation, increases expression	3
mercuric bromide	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
Particulate Matter	decreases expression, increases abundance	2
methylmercuric chloride	decreases expression	1
bisphenol A	decreases methylation	1
ferrous chloride	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	increases expression	1
Diazinon	increases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Malathion	increases expression	1
N-Nitrosopyrrolidine	increases expression	1
Tretinoin	decreases expression	1
Triclosan	increases expression	1
Vanadates	decreases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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