FAM72D

Summary

FAM72D (family with sequence similarity 72 member D, HGNC:33593) is a protein-coding gene on chromosome 1q21.1, encoding Protein FAM72D (Q6L9T8).

Located in cytosol and intracellular membrane-bounded organelle.

Source: NCBI Gene 728833 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_207418

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33593
Approved symbol	FAM72D
Name	family with sequence similarity 72 member D
Location	1q21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000215784
Ensembl biotype	protein_coding
OMIM	614712
Entrez	728833

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000400889, ENST00000936347

RefSeq mRNA: 1 — MANE Select: NM_207418 NM_207418

CCDS: CCDS72855

Canonical transcript exons

ENST00000400889 — 4 exons

Exon	Start	End
ENSE00001372125	145111503	145112696
ENSE00001404343	145095974	145096999
ENSE00001639141	145098988	145099065
ENSE00001891290	145103007	145103131

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 90.01.

FANTOM5 (CAGE): breadth broad, TPM avg 0.4669 / max 12.9298, expressed in 302 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
201665	0.4669	302

Top tissues by expression

133 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	90.01	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.93	gold quality
ventricular zone	UBERON:0003053	80.20	gold quality
ganglionic eminence	UBERON:0004023	71.86	gold quality
vermiform appendix	UBERON:0001154	70.45	gold quality
monocyte	CL:0000576	68.45	gold quality
lower esophagus mucosa	UBERON:0035834	67.86	gold quality
leukocyte	CL:0000738	67.85	gold quality
lymph node	UBERON:0000029	67.54	gold quality
bone marrow	UBERON:0002371	65.57	gold quality
placenta	UBERON:0001987	65.24	gold quality
endometrium	UBERON:0001295	63.98	gold quality
mucosa of transverse colon	UBERON:0004991	63.70	gold quality
stromal cell of endometrium	CL:0002255	62.62	gold quality
cerebellar hemisphere	UBERON:0002245	62.06	gold quality
cerebellar cortex	UBERON:0002129	61.99	gold quality
cerebellum	UBERON:0002037	61.87	gold quality
rectum	UBERON:0001052	61.46	gold quality
tonsil	UBERON:0002372	61.23	gold quality
duodenum	UBERON:0002114	61.16	gold quality
right hemisphere of cerebellum	UBERON:0014890	60.87	gold quality
spleen	UBERON:0002106	60.45	gold quality
esophagus mucosa	UBERON:0002469	60.45	gold quality
adrenal tissue	UBERON:0018303	60.18	gold quality
smooth muscle tissue	UBERON:0001135	59.36	gold quality
bone marrow cell	CL:0002092	59.18	silver quality
skin of leg	UBERON:0001511	58.83	gold quality
mucosa of stomach	UBERON:0001199	58.46	gold quality
zone of skin	UBERON:0000014	58.31	gold quality
granulocyte	CL:0000094	58.02	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.35
E-MTAB-6524	no	51.14
E-MTAB-6911	no	43.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting FAM72D, 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-1277-5P	100.00	73.95	5056
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-3658	99.96	73.87	4379
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-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-3059-5P	99.70	69.93	2491

Literature-anchored findings (GeneRIF, showing 2)

• An epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci (FAM72A, FAM72B, FAM72C, FAM72D). (PMID:26206078)
• The hydroxymethylome of multiple myeloma identifies FAM72D as a 1q21 marker linked to proliferation. (PMID:31221779)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	FAM72A	ENSDARG00000070621
mus_musculus	Fam72a	ENSMUSG00000055184
rattus_norvegicus	Fam72a	ENSRNOG00000042747

Paralogs (3): FAM72B (ENSG00000188610), FAM72A (ENSG00000196550), FAM72C (ENSG00000263513)

Protein

Protein identifiers

Protein FAM72D — Q6L9T8 (reviewed: Q6L9T8)

Alternative names: Gastric cancer up-regulated protein 2

All UniProt accessions (1): Q6L9T8

UniProt curated annotations — full annotation on UniProt →

Induction. Up-regulated in gastric cancer.

Similarity. Belongs to the FAM72 family.

RefSeq proteins (1): NP_997301* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026768	YPEH2ZP	Family

Pfam: PF14976

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6L9T8-F1	84.86	0.61

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): FISCHER_DREAM_TARGETS, chr1q21, TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C, MIR153_5P, MIR1277_5P, MIR3121_3P, MIR10527_5P, MIR4482_3P, MIR206, MIR1_3P, MIR330_3P, MIR613, MIR4680_3P, MIR4524A_3P, MIR361_3P

GO Biological Process (0):

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

GO Cellular Component (1): cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

560 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM72D	SRGAP2B	P0DMP2	691
FAM72D	ANKRD20A3P	Q5VUR7	474
FAM72D	ARHGAP11B	Q3KRB8	471
FAM72D	SRGAP2C	P0DJJ0	459
FAM72D	ZNG1C	Q5JTY5	449
FAM72D	ZNG1F	Q4V339	449
FAM72D	GTF2H2C	Q6P1K8	433
FAM72D	GTF2H2	Q13888	413
FAM72D	OTUD7A	Q8TE49	411
FAM72D	ARHGEF35	A5YM69	410
FAM72D	ZNG1A	Q9BRT8	406
FAM72D	ANKRD20A2P	Q5SQ80	400
FAM72D	ANKRD20A4P	Q4UJ75	399
FAM72D	GPHRA	B7ZAQ6	393
FAM72D	MTMR10	Q9NXD2	393

IntAct

10 interactions, top by confidence:

A	B	Type	Score
FAM72D	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
FAM72D	NTAQ1	psi-mi:“MI:0915”(physical association)	0.560
FAM72D	GOLGA7	psi-mi:“MI:0915”(physical association)	0.560
ZNF19	FAM72D	psi-mi:“MI:0915”(physical association)	0.560
NTAQ1	FAM72D	psi-mi:“MI:0915”(physical association)	0.000
FAM72D	GOLGA7	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): FAM72D (Two-hybrid), FAM72D (Two-hybrid), FAM72D (Two-hybrid), FAM72D (Affinity Capture-RNA), FAM72D (Affinity Capture-RNA)

ESM2 similar proteins: A1KXW8, A6QL50, E1BGQ2, H0Y354, O94955, P47224, Q08326, Q0IIH8, Q1JQA1, Q1RMS8, Q1RMZ1, Q2TBU5, Q3T1H6, Q4R372, Q4R528, Q4R9C4, Q5F480, Q5F4A1, Q5I0G3, Q5RCQ0, Q5RFG8, Q5TFE4, Q5TYM5, Q641X7, Q6L9T8, Q6PIP5, Q7L622, Q7Z6J8, Q7ZX59, Q86X60, Q8BFZ8, Q8BKW4, Q8BM85, Q8BX13, Q8CEL2, Q8N5C7, Q8N635, Q8NHU2, Q8TCF1, Q8TCJ0

Diamond homologs: A1KXW8, A6QL50, H0Y354, Q5TYM5, Q6L9T8, Q86X60, Q8BFZ8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

997 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:145096905:T:C	F20L	0.909
1:145096907:C:A	F20L	0.909
1:145096907:C:G	F20L	0.909
1:145103086:T:C	F104L	0.881
1:145103088:T:A	F104L	0.881
1:145103088:T:G	F104L	0.881
1:145096923:A:C	S26R	0.861
1:145096925:C:A	S26R	0.861
1:145096925:C:G	S26R	0.861
1:145096974:T:C	F43L	0.857
1:145096976:C:A	F43L	0.857
1:145096976:C:G	F43L	0.857
1:145103087:T:C	F104S	0.778
1:145103080:T:A	W102R	0.750
1:145103080:T:C	W102R	0.750
1:145098998:T:C	F55L	0.743
1:145099000:C:A	F55L	0.743
1:145099000:C:G	F55L	0.743
1:145096899:T:A	C18S	0.719
1:145096900:G:C	C18S	0.719
1:145096869:T:C	F8L	0.717
1:145096871:C:A	F8L	0.717
1:145096871:C:G	F8L	0.717
1:145096908:T:A	C21S	0.709
1:145096909:G:C	C21S	0.709
1:145099064:T:A	C77S	0.701
1:145099065:G:C	C77S	0.701
1:145099064:T:C	C77R	0.699
1:145099052:G:C	A73P	0.689
1:145099055:T:C	C74R	0.683

dbSNP variants (sampled 300 via entrez): RS10081803 (1:145100426 A>C), RS10465240 (1:145100045 C>T), RS1077771 (1:145109712 C>G), RS111453274 (1:145102734 C>G), RS111489598 (1:145099634 T>A,C), RS111640514 (1:145103707 T>C), RS112906161 (1:145093956 G>A,C,T), RS112984841 (1:145102078 A>T), RS113058626 (1:145098744 T>C,G), RS113384281 (1:145106565 A>G), RS1134005 (1:145103021 G>T), RS113575303 (1:145102071 A>C), RS1156257408 (1:145096939 A>G), RS1156435582 (1:145098559 C>T), RS1156850921 (1:145102012 A>G)

Disease associations

OMIM: gene MIM:614712 | 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

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	decreases expression, decreases methylation	2
propionaldehyde	decreases expression	1
perfluorooctanoic acid	decreases expression	1
diallyl trisulfide	decreases expression	1
M-VAC protocol	increases response to substance	1
beta-methylcholine	affects expression	1
2-palmitoylglycerol	increases expression	1
ICG 001	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
jinfukang	increases expression	1
incobotulinumtoxinA	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Dasatinib	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Cadmium	decreases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Catechin	decreases expression, affects cotreatment	1
Cisplatin	decreases expression	1
Hydrogen Peroxide	affects expression	1
Mustard Gas	decreases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Oxygen	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Testosterone	decreases expression, affects cotreatment	1
Tretinoin	decreases expression	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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