FAM53A

Summary

FAM53A (family with sequence similarity 53 member A, HGNC:31860) is a protein-coding gene on chromosome 4p16.3, encoding Protein FAM53A (Q6NSI3). May play an important role in neural development; the dorsomedial roof of the third ventricle.

Predicted to be involved in protein import into nucleus. Predicted to be active in nucleus.

Source: NCBI Gene 152877 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 126 total — 2 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_001174070

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31860
Approved symbol	FAM53A
Name	family with sequence similarity 53 member A
Location	4p16.3
Locus type	gene with protein product
Status	Approved
Aliases	DNTNP
Ensembl gene	ENSG00000174137
Ensembl biotype	protein_coding
OMIM	617229
Entrez	152877

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 retained_intron

ENST00000308132, ENST00000461064, ENST00000467215, ENST00000472884, ENST00000489029, ENST00000489363

RefSeq mRNA: 3 — MANE Select: NM_001174070 NM_001013622, NM_001174070, NM_001297435

CCDS: CCDS33939, CCDS75091

Canonical transcript exons

ENST00000308132 — 5 exons

Exon	Start	End
ENSE00001199412	1654978	1655723
ENSE00001266243	1657408	1657468
ENSE00002054040	1668667	1668905
ENSE00002223634	1684233	1684313
ENSE00002317633	1639887	1641607

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 87.36.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	87.36	gold quality
right testis	UBERON:0004534	84.33	gold quality
left testis	UBERON:0004533	83.47	gold quality
testis	UBERON:0000473	81.36	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.96	gold quality
secondary oocyte	CL:0000655	78.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.60	gold quality
adenohypophysis	UBERON:0002196	73.94	gold quality
pituitary gland	UBERON:0000007	73.86	gold quality
left lobe of thyroid gland	UBERON:0001120	73.66	gold quality
right lobe of thyroid gland	UBERON:0001119	73.64	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	72.93	gold quality
thyroid gland	UBERON:0002046	72.49	gold quality
spinal cord	UBERON:0002240	71.46	gold quality
adult organism	UBERON:0007023	68.30	gold quality
granulocyte	CL:0000094	67.95	gold quality
stromal cell of endometrium	CL:0002255	67.19	gold quality
right lobe of liver	UBERON:0001114	67.09	gold quality
popliteal artery	UBERON:0002250	66.87	gold quality
tibial artery	UBERON:0007610	66.87	gold quality
lower esophagus	UBERON:0013473	66.07	gold quality
lower esophagus muscularis layer	UBERON:0035833	66.06	gold quality
substantia nigra	UBERON:0002038	65.86	gold quality
muscle layer of sigmoid colon	UBERON:0035805	65.69	gold quality
aorta	UBERON:0000947	65.40	gold quality
palpebral conjunctiva	UBERON:0001812	65.39	gold quality
gastrocnemius	UBERON:0001388	65.28	gold quality
lower esophagus mucosa	UBERON:0035834	65.15	gold quality
right hemisphere of cerebellum	UBERON:0014890	65.14	gold quality
midbrain	UBERON:0001891	64.97	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting FAM53A, 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-513A-5P	100.00	69.77	2465
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577

Literature-anchored findings (GeneRIF, showing 1)

• Expression levels of TP53BP2, FBXO28, and FAM53A genes were associated with patient survival specifically in ER-positive, TP53-mutated tumors. (PMID:28179588)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam53a	ENSMUSG00000037339
rattus_norvegicus	Fam53a	ENSRNOG00000017548

Paralogs (2): FAM53C (ENSG00000120709), FAM53B (ENSG00000189319)

Protein

Protein identifiers

Protein FAM53A — Q6NSI3 (reviewed: Q6NSI3)

Alternative names: Dorsal neural-tube nuclear protein

All UniProt accessions (3): Q6NSI3, C9JYQ7, H0Y9F1

UniProt curated annotations — full annotation on UniProt →

Function. May play an important role in neural development; the dorsomedial roof of the third ventricle.

Subcellular location. Nucleus.

Similarity. Belongs to the FAM53 family.

RefSeq proteins (3): NP_001013644, NP_001167541, NP_001284364 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029356	FAM53	Family

Pfam: PF15242

UniProt features (13 total): compositionally biased region 5, modified residue 3, region of interest 2, chain 1, sequence conflict 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6NSI3-F1	53.27	0.00

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 (3): 301, 304, 125

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_NUCLEAR_TRANSPORT, chr4p16, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, RASHI_RESPONSE_TO_IONIZING_RADIATION_5, GOBP_PROTEIN_LOCALIZATION_TO_NUCLEUS, GOBP_INTRACELLULAR_TRANSPORT, GOBP_IMPORT_INTO_NUCLEUS, GSE14415_NATURAL_TREG_VS_FOXP3_KO_NATURAL_TREG_DN, GSE10240_CTRL_VS_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, NCOA6_TARGET_GENES, SKIL_TARGET_GENES, SYNCRIP_TARGET_GENES

GO Biological Process (1): protein import into nucleus (GO:0006606)

GO Molecular Function (0):

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular protein transport	1
protein localization to nucleus	1
import into nucleus	1
establishment of protein localization to organelle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

400 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM53A	TMEM129	A0AVI4	654
FAM53A	SLBP	Q14493	516
FAM53A	TACC3	Q9Y6A5	498
FAM53A	Q8N1N5	Q8N1N5	474
FAM53A	SLC35D4	Q24JQ0	459
FAM53A	CLLU1-AS1	Q5K130	431
FAM53A	IGFL1	Q6UW32	411
FAM53A	GTF3C3	Q9Y5Q9	410
FAM53A	FCAMR	Q8WWV6	406
FAM53A	LETM1	O95202	391
FAM53A	SLC44A2	Q8IWA5	389
FAM53A	GTF2E1	P29083	381
FAM53A	ZNF716	A6NP11	376
FAM53A	ZNF439	Q8NDP4	374
FAM53A	EVC2	Q86UK5	374

IntAct

0 interactions, top by confidence:

BioGRID (4): FAM53A (Affinity Capture-RNA), FAM53A (Affinity Capture-RNA), FAM53A (Affinity Capture-RNA), APP (Reconstituted Complex)

ESM2 similar proteins: A2AI08, A5D962, A7YWL5, B0BN13, E9PV82, F1QGH6, O94983, P70298, Q0IHB0, Q1L899, Q2T9L4, Q3U1J1, Q3U2K0, Q5HZN9, Q5JTD0, Q5JXC2, Q5PQ25, Q5U5E5, Q5XHX2, Q68DK7, Q6NSI3, Q6P9J5, Q6PDH0, Q6PDM1, Q6T4R5, Q7TNY7, Q80Y50, Q86UU1, Q8BG26, Q8BG80, Q8BP99, Q8BRV5, Q8BSN5, Q8CD60, Q8JZX9, Q8K3I4, Q8NFW9, Q8TAB5, Q91V27, Q922B9

Diamond homologs: E9PV82, F1QN48, H2M146, Q14153, Q29RM2, Q5R815, Q5ZKN5, Q6NSI3, Q8BGR5, Q8BXQ8, Q9NYF3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	1
Uncertain significance	93
Likely benign	12
Benign	10

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
1075075	NC_000004.11:g.(?1619775)(2181192_?)del	Pathogenic
395188	GRCh37/hg19 4p16.3(chr4:29214-1925508)x1	Pathogenic
983182	GRCh37/hg19 4p16.3(chr4:1420948-1836794)x3	Likely pathogenic

SpliceAI

1630 predictions. Top by Δscore:

Variant	Effect	Δscore
4:1655719:CTGGT:C	acceptor_gain	1.0000
4:1655720:TGGT:T	acceptor_gain	1.0000
4:1655725:T:A	acceptor_loss	1.0000
4:1657465:GCAAC:G	acceptor_loss	1.0000
4:1657466:CAA:C	acceptor_gain	1.0000
4:1657467:AACTG:A	acceptor_loss	1.0000
4:1657468:ACTGA:A	acceptor_loss	1.0000
4:1657469:C:CC	acceptor_gain	1.0000
4:1657469:CTGA:C	acceptor_loss	1.0000
4:1657470:T:G	acceptor_loss	1.0000
4:1668662:CTTA:C	donor_loss	1.0000
4:1668665:ACCG:A	donor_loss	1.0000
4:1668666:CCGGG:C	donor_gain	1.0000
4:1668914:C:CT	acceptor_gain	1.0000
4:1668915:A:T	acceptor_gain	1.0000
4:1641603:AAAGT:A	acceptor_gain	0.9900
4:1641604:AAGT:A	acceptor_gain	0.9900
4:1641606:GT:G	acceptor_gain	0.9900
4:1641607:TCTG:T	acceptor_loss	0.9900
4:1641608:C:CC	acceptor_gain	0.9900
4:1641609:T:A	acceptor_loss	0.9900
4:1654972:CCTCA:C	donor_loss	0.9900
4:1654973:CTCA:C	donor_loss	0.9900
4:1654974:TCACC:T	donor_loss	0.9900
4:1654975:CAC:C	donor_loss	0.9900
4:1654976:A:T	donor_loss	0.9900
4:1654977:C:CA	donor_loss	0.9900
4:1655721:GGT:G	acceptor_gain	0.9900
4:1655722:GT:G	acceptor_gain	0.9900
4:1655724:C:CC	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000003136 (4:1677118 G>C,T), RS1000071735 (4:1640016 C>A), RS1000084510 (4:1665340 T>C), RS1000131468 (4:1659113 C>T), RS1000142259 (4:1606447 G>A,C), RS1000147337 (4:1612980 C>G,T), RS1000151683 (4:1577140 G>A), RS1000182580 (4:1684663 C>T), RS1000182795 (4:1621927 T>C), RS1000183774 (4:1646792 T>A), RS1000193827 (4:1580325 G>A,C), RS1000249275 (4:1580315 C>A,G), RS1000293890 (4:1643103 T>C), RS10003193 (4:1621657 C>T), RS1000321791 (4:1645684 T>C)

Disease associations

OMIM: gene MIM:617229 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST008460_9	Gout vs. Hyperuricemia	9.000000e-07
GCST008525_3	Artificially sweetened beverage consumption	4.000000e-06
GCST010699_17	Brain morphology (min-P)	5.000000e-10
GCST010701_28	Cortical surface area (MOSTest)	3.000000e-32
GCST010702_46	Subcortical volume (MOSTest)	5.000000e-10
GCST010703_270	Brain morphology (MOSTest)	5.000000e-13
GCST012227_1015	Hip circumference adjusted for BMI	2.000000e-08
GCST90020028_1700	Hip circumference adjusted for BMI	8.000000e-09
GCST90020028_1701	Hip circumference adjusted for BMI	5.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0009104	hyperuricemia
EFO:0010096	artificially sweetened beverage consumption measurement
EFO:0004346	neuroimaging measurement
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic	affects methylation, increases methylation	2
Ozone	affects cotreatment, decreases expression, affects methylation, increases abundance	2
Valproic Acid	increases methylation, increases expression	2
aristolochic acid I	increases expression	1
trichostatin A	increases expression	1
zinc chromate	increases abundance, decreases expression	1
ferrous chloride	decreases expression	1
aflatoxin B2	decreases methylation	1
methacrylaldehyde	decreases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
abrine	decreases expression	1
jinfukang	increases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, decreases expression	1
Air Pollutants	affects methylation, increases abundance	1
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	1
Methyl Methanesulfonate	increases expression	1
Triclosan	increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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