FAM149A

Summary

FAM149A (family with sequence similarity 149 member A, HGNC:24527) is a protein-coding gene on chromosome 4q35.1, encoding Protein FAM149A (A5PLN7).

At a glance

• Clinical variants (ClinVar): 117 total
• MANE Select transcript: NM_001395294

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24527
Approved symbol	FAM149A
Name	family with sequence similarity 149 member A
Location	4q35.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP564J102, MST119, MSTP119
Ensembl gene	ENSG00000109794
Ensembl biotype	protein_coding
Entrez	25854

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 13 protein_coding, 4 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000227065, ENST00000389354, ENST00000502894, ENST00000502970, ENST00000503432, ENST00000504330, ENST00000508379, ENST00000509574, ENST00000510790, ENST00000510843, ENST00000512271, ENST00000513030, ENST00000513212, ENST00000514153, ENST00000514829, ENST00000514956, ENST00000515078, ENST00000706927, ENST00000850903

RefSeq mRNA: 6 — MANE Select: NM_001395294 NM_001006655, NM_001350178, NM_001350179, NM_001367768, NM_001395294, NM_015398

CCDS: CCDS34117, CCDS93680

Canonical transcript exons

ENST00000706927 — 14 exons

Exon	Start	End
ENSE00001700974	186167184	186167262
ENSE00003477929	186149173	186149283
ENSE00003528081	186153645	186153770
ENSE00003562304	186156000	186156190
ENSE00003572845	186162845	186162948
ENSE00003574053	186151903	186152045
ENSE00003610487	186154468	186154638
ENSE00003670900	186163424	186163633
ENSE00003673311	186157565	186157719
ENSE00003730008	186166968	186167096
ENSE00003750365	186165344	186165464
ENSE00003924894	186104704	186105642
ENSE00003935079	186149566	186149704
ENSE00003938511	186171914	186175337

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 95.44.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7550 / max 37.8235, expressed in 679 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
50895	1.3312	574
50894	0.2232	126
50893	0.2006	116

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	95.44	gold quality
secondary oocyte	CL:0000655	94.38	gold quality
nucleus accumbens	UBERON:0001882	92.95	gold quality
bronchial epithelial cell	CL:0002328	92.80	gold quality
right lobe of liver	UBERON:0001114	92.37	gold quality
pancreatic ductal cell	CL:0002079	92.13	gold quality
epithelium of bronchus	UBERON:0002031	91.81	gold quality
buccal mucosa cell	CL:0002336	91.51	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.35	gold quality
bronchus	UBERON:0002185	91.14	gold quality
amygdala	UBERON:0001876	91.11	gold quality
putamen	UBERON:0001874	90.69	gold quality
caudate nucleus	UBERON:0001873	90.67	gold quality
nephron tubule	UBERON:0001231	90.11	gold quality
right frontal lobe	UBERON:0002810	89.94	gold quality
cortical plate	UBERON:0005343	89.67	gold quality
body of pancreas	UBERON:0001150	89.64	gold quality
liver	UBERON:0002107	89.61	gold quality
temporal lobe	UBERON:0001871	89.26	gold quality
Ammon’s horn	UBERON:0001954	89.21	gold quality
metanephros cortex	UBERON:0010533	88.99	gold quality
fundus of stomach	UBERON:0001160	88.92	gold quality
cingulate cortex	UBERON:0003027	88.61	gold quality
adult mammalian kidney	UBERON:0000082	88.58	gold quality
gall bladder	UBERON:0002110	88.41	gold quality
ganglionic eminence	UBERON:0004023	88.35	gold quality
anterior cingulate cortex	UBERON:0009835	88.35	gold quality
renal medulla	UBERON:0000362	88.31	gold quality
entorhinal cortex	UBERON:0002728	88.14	gold quality
telencephalon	UBERON:0001893	87.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting FAM149A, 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-3120-5P	100.00	65.56	965
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-6513-3P	99.59	69.77	1102
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-520E-5P	99.27	68.90	1513
HSA-MIR-4326	98.97	67.63	962
HSA-MIR-6769B-5P	98.73	64.91	1092

Literature-anchored findings (GeneRIF, showing 2)

• In total, 270,389 single nucleotide polymorphisms passed quality control, and 4 SNPs in the FAM149A gene were associated with Acute Mountain Sickness; however, in the validation cohorts, FAM149A was not associated with the presence or severity of AMS. (PMID:26600424)
• Whole exome sequencing identified FAM149A as a plausible causative gene for congenital hereditary endothelial dystrophy, affecting Nrf2-Antioxidant signaling upon oxidative stress. (PMID:34303830)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam149a	ENSDARG00000073709
mus_musculus	Fam149a	ENSMUSG00000070044
rattus_norvegicus	Fam149a	ENSRNOG00000021693

Paralogs (1): FAM149B1 (ENSG00000138286)

Protein

Protein identifiers

Protein FAM149A — A5PLN7 (reviewed: A5PLN7)

All UniProt accessions (8): A5PLN7, A0A0A0MRZ3, D6RAL4, D6RC92, D6RGX1, H0Y8Y9, H0Y909, H0Y965

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM149 family.

Isoforms (4)

UniProt ID	Names	Canonical?
A5PLN7-1	1	yes
A5PLN7-2	2
A5PLN7-3	3
A5PLN7-4	4

RefSeq proteins (6): NP_001006656, NP_001337107, NP_001337108, NP_001354697, NP_001382223, NP_056213 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022194	DUF3719	Domain
IPR039630	FAM149	Family

Pfam: PF12516

UniProt features (22 total): sequence variant 6, region of interest 4, sequence conflict 4, compositionally biased region 4, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A5PLN7-F1	50.07	0.04

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, CAIRO_HEPATOBLASTOMA_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, chr4q35, NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN, CERVERA_SDHB_TARGETS_1_UP, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_MCV6_ICP_WITH_H3K27ME3, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, MIKKELSEN_ES_ICP_WITH_H3K4ME3, LEE_BMP2_TARGETS_DN, MAFG_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

680 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM149A	TRIML1	Q8N9V2	583
FAM149A	FRG1	Q14331	581
FAM149A	FRG2	Q64ET8	506
FAM149A	CYP4V2	Q6ZWL3	483
FAM149A	CCDC110	Q8TBZ0	475
FAM149A	STOX2	Q9P2F5	474
FAM149A	CFAP96	A7E2U8	459
FAM149A	SORBS2	O94875	447
FAM149A	CFAP97	Q9P2B7	445
FAM149A	TRIML2	Q8N7C3	440
FAM149A	R3HCC1	Q9Y3T6	439
FAM149A	MOCS1	Q9NZB8	427
FAM149A	SERGEF	Q9UGK8	426
FAM149A	PAPLN	O95428	410
FAM149A	ZFP42	Q96MM3	400

IntAct

2 interactions, top by confidence:

A	B	Type	Score
TESC	FAM149A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): FAM149A (Affinity Capture-RNA), FAM149A (Proximity Label-MS)

ESM2 similar proteins: A0JNF3, A1L253, A2AHC3, A3KP40, A5PLN7, A5WUN7, A6H5Y1, B1AXH1, B2GUZ2, D3Z8E6, E9PV87, E9Q309, H6D7E6, O14513, O60303, P0CAX8, P28290, Q14B48, Q1G7G9, Q2KHM9, Q32LN6, Q49A88, Q566N9, Q5HYW2, Q5PQL8, Q5REU9, Q5T5Y3, Q5VT06, Q60664, Q66H35, Q66MI6, Q6A000, Q6AYP4, Q6NSV7, Q6NXP0, Q6ZRS4, Q6ZVD7, Q80VP2, Q8BJS7, Q8CB14

Diamond homologs: A0JNF3, A1L253, A5PLN7, Q5PQL8, Q6NSV7, Q8CFV2, Q96BN6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	84
Likely benign	17
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3411 predictions. Top by Δscore:

Variant	Effect	Δscore
4:186147967:T:G	acceptor_gain	1.0000
4:186149171:A:AG	acceptor_gain	1.0000
4:186149172:G:GA	acceptor_gain	1.0000
4:186149172:GAA:G	acceptor_gain	1.0000
4:186149172:GAAGA:G	acceptor_gain	1.0000
4:186154600:A:T	donor_gain	1.0000
4:186154609:G:GT	donor_gain	1.0000
4:186154634:GAGGA:G	donor_gain	1.0000
4:186154636:G:GT	donor_gain	1.0000
4:186154636:GGA:G	donor_gain	1.0000
4:186154637:GA:G	donor_gain	1.0000
4:186154637:GAG:G	donor_gain	1.0000
4:186154639:G:GG	donor_gain	1.0000
4:186155998:A:AG	acceptor_gain	1.0000
4:186155998:AGT:A	acceptor_gain	1.0000
4:186155999:G:GG	acceptor_gain	1.0000
4:186155999:GT:G	acceptor_gain	1.0000
4:186155999:GTG:G	acceptor_gain	1.0000
4:186155999:GTGAT:G	acceptor_gain	1.0000
4:186156189:AG:A	donor_loss	1.0000
4:186156190:GGTAC:G	donor_loss	1.0000
4:186156191:G:A	donor_loss	1.0000
4:186156192:T:A	donor_loss	1.0000
4:186166967:GTACA:G	acceptor_gain	1.0000
4:186104516:GCTGG:G	donor_gain	0.9900
4:186104519:GG:G	donor_gain	0.9900
4:186104519:GGGT:G	donor_loss	0.9900
4:186104520:GG:G	donor_gain	0.9900
4:186104521:G:GA	donor_loss	0.9900
4:186104522:T:G	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000009613 (4:186142692 A>C,G), RS1000034332 (4:186134393 T>G), RS1000059101 (4:186148513 C>T), RS1000124193 (4:186150009 G>A,C), RS1000174645 (4:186103622 G>C), RS1000229174 (4:186118000 T>G), RS1000246288 (4:186144952 G>A,T), RS1000246948 (4:186146337 C>T), RS1000359286 (4:186159132 T>C), RS1000401165 (4:186119016 A>G), RS1000428829 (4:186104473 C>A,G,T), RS1000467544 (4:186129026 T>C), RS1000469966 (4:186164943 C>T), RS1000500305 (4:186129244 T>C), RS1000516257 (4:186153028 T>C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

44 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, increases methylation, affects expression, decreases expression	6
trichostatin A	decreases expression, increases expression, affects cotreatment	3
mercuric bromide	affects cotreatment, decreases expression	2
Vorinostat	affects cotreatment, decreases expression	2
Panobinostat	decreases expression, affects cotreatment	2
Estradiol	affects cotreatment, increases expression, decreases expression	2
Nickel	decreases expression	2
Cyclosporine	decreases expression, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
decabromobiphenyl ether	affects expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Carbamazepine	affects expression	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1

Clinical trials (associated diseases)

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