HDGFL1

Summary

HDGFL1 (HDGF like 1, HGNC:21095) is a protein-coding gene on chromosome 6p22.3, encoding Hepatoma-derived growth factor-like protein 1 (Q5TGJ6).

Predicted to be involved in chromatin remodeling. Predicted to be active in nucleus.

Source: NCBI Gene 154150 — RefSeq curated summary.

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 54 total
• MANE Select transcript: NM_138574

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21095
Approved symbol	HDGFL1
Name	HDGF like 1
Location	6p22.3
Locus type	gene with protein product
Status	Approved
Aliases	dJ309H15.1, Hdgfrp1, HRP-1
Ensembl gene	ENSG00000112273
Ensembl biotype	protein_coding
Entrez	154150

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000510882

RefSeq mRNA: 1 — MANE Select: NM_138574 NM_138574

CCDS: CCDS34347

Canonical transcript exons

ENST00000510882 — 1 exons

Exon	Start	End
ENSE00002081119	22569566	22571666

Expression profiles

Bgee: expression breadth broad, 52 present calls, max score 96.49.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4416 / max 392.4439, expressed in 6 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66367	0.3145	6
66366	0.1161	4
66365	0.0109	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	96.49	gold quality
left testis	UBERON:0004533	95.84	gold quality
right testis	UBERON:0004534	95.76	gold quality
adult organism	UBERON:0007023	93.49	gold quality
testis	UBERON:0000473	93.02	gold quality
cardiac muscle of right atrium	UBERON:0003379	90.77	gold quality
secondary oocyte	CL:0000655	90.57	gold quality
ileal mucosa	UBERON:0000331	90.54	silver quality
tibialis anterior	UBERON:0001385	90.36	silver quality
left ventricle myocardium	UBERON:0006566	90.03	gold quality
pancreatic ductal cell	CL:0002079	88.04	silver quality
oocyte	CL:0000023	87.85	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.14	gold quality
upper arm skin	UBERON:0004263	83.90	gold quality
deltoid	UBERON:0001476	83.23	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.61	gold quality
cardia of stomach	UBERON:0001162	79.57	silver quality
kidney epithelium	UBERON:0004819	79.55	gold quality
vena cava	UBERON:0004087	79.36	silver quality
quadriceps femoris	UBERON:0001377	78.04	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	77.19	gold quality
nasal cavity epithelium	UBERON:0005384	77.14	gold quality
myocardium	UBERON:0002349	77.02	gold quality
mucosa of paranasal sinus	UBERON:0005030	76.49	gold quality
vastus lateralis	UBERON:0001379	76.34	gold quality
ventral tegmental area	UBERON:0002691	76.15	silver quality
pharyngeal mucosa	UBERON:0000355	76.05	silver quality
pons	UBERON:0000988	75.14	silver quality
superior surface of tongue	UBERON:0007371	75.10	silver quality
inferior vagus X ganglion	UBERON:0005363	74.99	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting HDGFL1, 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-4283	100.00	66.42	2097
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-7160-5P	99.11	67.17	2207

Literature-anchored findings (GeneRIF, showing 1)

• The segment encompassed only one UCSC (University of California-Santa Cruz genome bioinformatics database) gene: HDGFL1 (Homo sapiens hepatoma derived growth factor like 1, GB #AL033539). (PMID:20509080)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Hdgfl1	ENSMUSG00000045835

Paralogs (4): HDGF (ENSG00000143321), PSIP1 (ENSG00000164985), HDGFL3 (ENSG00000166503), HDGFL2 (ENSG00000167674)

Protein

Protein identifiers

Hepatoma-derived growth factor-like protein 1 — Q5TGJ6 (reviewed: Q5TGJ6)

Alternative names: PWWP domain-containing protein 1

All UniProt accessions (2): Q5TGJ6, A0A140VJK8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the HDGF family.

RefSeq proteins (1): NP_612641* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000313	PWWP_dom	Domain

Pfam: PF00855

UniProt features (12 total): sequence conflict 4, compositionally biased region 4, chain 1, domain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5TGJ6-F1	65.59	0.31

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): WANG_RESPONSE_TO_BEXAROTENE_UP, GOBP_CHROMATIN_REMODELING, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, MIKKELSEN_ES_ICP_WITH_H3K4ME3, GCNP_SHH_UP_EARLY.V1_UP, WNT_UP.V1_DN, NFKBIA_TARGET_GENES, GSE11818_WT_VS_DICER_KO_TREG_UP, GSE9946_IMMATURE_VS_MATURE_STIMULATORY_DC_DN, GSE12505_WT_VS_E2_2_HET_PDC_UP, GSE12507_PDC_CELL_LINE_VS_IMMATUE_T_CELL_LINE_DN, GSE13173_UNTREATED_VS_IL12_TREATED_ACT_CD8_TCELL_UP, GSE14413_UNSTIM_VS_IFNB_STIM_L929_CELLS_DN, GSE13887_RESTING_VS_NO_TREATED_CD4_TCELL_UP, GOBP_CHROMATIN_ORGANIZATION

GO Biological Process (1): chromatin remodeling (GO:0006338)

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
chromatin organization	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

594 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HDGFL1	NUCLEOLIN	P19338	747
HDGFL1	NSD3	Q9BZ95	549
HDGFL1	IGF2BP3	O00425	523
HDGFL1	CTBP1	Q13363	517
HDGFL1	DDX5	P17844	493
HDGFL1	CTBP2	P56545	476
HDGFL1	AZU1	P20160	434
HDGFL1	PWWP2B	Q6NUJ5	420
HDGFL1	AGER	Q15109	420
HDGFL1	CDCA7L	Q96GN5	392
HDGFL1	METTL3	Q86U44	391
HDGFL1	TNF	P01375	356
HDGFL1	SMYD1	Q8NB12	348
HDGFL1	CROT	Q9UKG9	344
HDGFL1	PTN	P21246	331

IntAct

0 interactions, top by confidence:

BioGRID (2): HDGFL1 (Positive Genetic), HDGFL1 (Affinity Capture-MS)

ESM2 similar proteins: A4IFM7, A8C984, B6D5P1, B6D5P6, E9PT87, O08815, O54988, O55092, O70551, O88831, P00519, P00520, P00521, P07313, P0C865, P13234, P20689, P42684, P46087, Q13164, Q14028, Q16566, Q2KI23, Q32MK0, Q3SYS4, Q3UH66, Q3UIZ8, Q3ULB5, Q4JIM5, Q4KMM3, Q4V8B0, Q5R8Z4, Q5RDG7, Q5TGJ6, Q63553, Q6AYH9, Q6PDI6, Q80XI3, Q8BHL3, Q8BWQ5

Diamond homologs: A4FUF0, F4IN78, F4IZM8, O75475, P51858, P51859, Q175F8, Q29NG1, Q32N87, Q3UMU9, Q49A26, Q562D5, Q5R7T2, Q5RKH0, Q5RKN4, Q5TGJ6, Q5XXA7, Q5XXA9, Q5ZLS7, Q66T72, Q6P4K1, Q7Q161, Q7Z4V5, Q812D1, Q8MJG1, Q8VHK7, Q922P9, Q923W4, Q925G1, Q99JF8, Q9JMG7, Q9LEY4, Q9XER9, Q9XSK7, Q9Y3E1, Q8T079, F4I907, Q9LSV0, P54276, P77161

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

89 predictions. Top by Δscore:

Variant	Effect	Δscore
6:22570156:A:T	donor_gain	0.7400
6:22570272:G:GT	donor_gain	0.6200
6:22570083:G:GT	donor_gain	0.5900
6:22570059:G:GT	donor_gain	0.5600
6:22570080:G:GT	donor_gain	0.5500
6:22570155:G:GT	donor_gain	0.5300
6:22570251:G:GT	donor_gain	0.5100
6:22570254:G:GT	donor_gain	0.5100
6:22570250:G:GT	donor_gain	0.5000
6:22570239:G:GT	donor_gain	0.4600
6:22570251:G:T	donor_gain	0.4400
6:22570255:A:T	donor_gain	0.4400
6:22570404:G:GT	donor_gain	0.4400
6:22570236:G:GT	donor_gain	0.4300
6:22570266:G:GT	donor_gain	0.4300
6:22570154:GGAGA:G	donor_gain	0.4200
6:22570107:G:GT	donor_gain	0.4100
6:22570300:C:T	donor_gain	0.4000
6:22570177:TG:T	donor_gain	0.3900
6:22570178:GG:G	donor_gain	0.3900
6:22570174:C:CA	acceptor_gain	0.3800
6:22570324:GCCT:G	donor_gain	0.3800
6:22570290:C:T	donor_gain	0.3700
6:22570347:G:GT	donor_gain	0.3700
6:22570157:GA:G	donor_gain	0.3600
6:22570159:G:GG	donor_gain	0.3600
6:22570161:C:A	donor_gain	0.3600
6:22570328:G:GG	donor_gain	0.3600
6:22570330:A:AT	donor_gain	0.3600
6:22569993:G:GT	donor_gain	0.3500

AlphaMissense

1657 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:22569621:T:C	F16L	1.000
6:22569623:T:A	F16L	1.000
6:22569623:T:G	F16L	1.000
6:22569650:G:C	W25C	0.999
6:22569650:G:T	W25C	0.999
6:22569651:C:T	P26S	0.999
6:22569699:T:C	F42L	0.999
6:22569700:T:C	F42S	0.999
6:22569701:C:A	F42L	0.999
6:22569701:C:G	F42L	0.999
6:22569702:T:C	F43L	0.999
6:22569704:C:A	F43L	0.999
6:22569704:C:G	F43L	0.999
6:22569798:T:C	F75L	0.999
6:22569799:T:C	F75S	0.999
6:22569800:C:A	F75L	0.999
6:22569800:C:G	F75L	0.999
6:22569622:T:C	F16S	0.998
6:22569622:T:G	F16C	0.998
6:22569648:T:A	W25R	0.998
6:22569648:T:C	W25R	0.998
6:22569652:C:A	P26Q	0.998
6:22569702:T:A	F43I	0.998
6:22569706:G:A	G44E	0.998
6:22569621:T:A	F16I	0.997
6:22569621:T:G	F16V	0.997
6:22569651:C:A	P26T	0.997
6:22569696:T:C	F41L	0.997
6:22569698:T:A	F41L	0.997
6:22569698:T:G	F41L	0.997

dbSNP variants (sampled 300 via entrez): RS1000464669 (6:22570748 C>G), RS1000502278 (6:22569112 G>A), RS1001535947 (6:22568167 A>G), RS1002135267 (6:22571746 G>A), RS1002470459 (6:22570476 G>A), RS1002563895 (6:22570354 C>A,T), RS1004347313 (6:22571560 C>T), RS1004580542 (6:22569213 A>T), RS1004654192 (6:22569426 G>A,C,T), RS1004668002 (6:22570506 C>T), RS1005019426 (6:22570892 A>G), RS1005582896 (6:22570141 C>A,G), RS1006286894 (6:22569863 C>G,T), RS1006650855 (6:22568264 A>G), RS1006664683 (6:22571303 C>A,G)

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

15 associations (top):

Study	Trait	p-value
GCST002800_2	Number of children (6+ vs. 0 or 1)	1.000000e-06
GCST004750_77	Squamous cell lung carcinoma	3.000000e-06
GCST004787_9	Coronary artery disease (myocardial infarction, percutaneous transluminal coronary angioplasty, coronary artery bypass grafting, angina or chromic ischemic heart disease)	2.000000e-09
GCST008114_27	Type 2 diabetes	2.000000e-06
GCST009391_901	Metabolite levels	7.000000e-06
GCST010002_49	Refractive error	6.000000e-38
GCST010320_113	PR interval	4.000000e-15
GCST010321_9	PR interval	6.000000e-18
GCST010479_73	Coronary artery disease	5.000000e-09
GCST010796_5327	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-09
GCST010796_5328	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-08
GCST010796_5329	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-08
GCST010866_110	Coronary artery disease	3.000000e-18
GCST010989_260	Body size at age 10	2.000000e-09
GCST011365_130	Myocardial infarction	2.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0006918	female fertility
EFO:0010441	triacylglycerol 58:7 measurement
EFO:0004462	PR interval
EFO:0004327	electrocardiography
EFO:0009819	comparative body size at age 10, self-reported

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, increases abundance	2
Valproic Acid	affects cotreatment, increases expression, decreases methylation	2
Cadmium Chloride	increases expression, increases abundance	2
Particulate Matter	increases abundance, decreases expression	2
CGP 52608	increases reaction, affects binding	1
bisphenol S	decreases methylation	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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