FAM72C

Summary

FAM72C (family with sequence similarity 72 member C, HGNC:30602) is a protein-coding gene on chromosome 1q21.1, encoding Protein FAM72C (H0Y354).

Located in cytosol and intracellular membrane-bounded organelle.

Source: NCBI Gene 554282 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_001287385

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30602
Approved symbol	FAM72C
Name	family with sequence similarity 72 member C
Location	1q21.1
Locus type	gene with protein product
Status	Approved
Aliases	RP5-998N21.9
Ensembl gene	ENSG00000263513
Ensembl biotype	protein_coding
OMIM	616853
Entrez	554282

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000369175, ENST00000584486, ENST00000931575, ENST00000931576

RefSeq mRNA: 3 — MANE Select: NM_001287385 NM_001287385, NM_001346070, NM_001346071

CCDS: CCDS72850, CCDS86008

Canonical transcript exons

ENST00000584486 — 4 exons

Exon	Start	End
ENSE00001641767	143955287	143956481
ENSE00003472164	143964855	143964979
ENSE00003600104	143968924	143969001
ENSE00003918733	143970990	143971986

Expression profiles

Bgee: expression breadth ubiquitous, 115 present calls, max score 85.86.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5495 / max 37.3756, expressed in 680 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
201666	1.5495	680
201665	0.4669	302

Top tissues by expression

118 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	85.86	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.61	gold quality
lymph node	UBERON:0000029	70.55	gold quality
ventricular zone	UBERON:0003053	70.03	gold quality
ganglionic eminence	UBERON:0004023	67.30	gold quality
stromal cell of endometrium	CL:0002255	64.61	gold quality
vermiform appendix	UBERON:0001154	63.08	gold quality
endometrium	UBERON:0001295	61.96	gold quality
lower esophagus mucosa	UBERON:0035834	61.63	gold quality
bone marrow	UBERON:0002371	60.56	gold quality
esophagus mucosa	UBERON:0002469	59.98	gold quality
adrenal tissue	UBERON:0018303	58.65	gold quality
mucosa of transverse colon	UBERON:0004991	58.07	gold quality
cerebellar cortex	UBERON:0002129	57.63	gold quality
rectum	UBERON:0001052	57.55	gold quality
cerebellum	UBERON:0002037	57.49	gold quality
cerebellar hemisphere	UBERON:0002245	57.40	gold quality
duodenum	UBERON:0002114	56.43	gold quality
right hemisphere of cerebellum	UBERON:0014890	56.01	gold quality
monocyte	CL:0000576	55.47	gold quality
spleen	UBERON:0002106	55.44	gold quality
granulocyte	CL:0000094	55.42	gold quality
leukocyte	CL:0000738	55.06	gold quality
smooth muscle tissue	UBERON:0001135	54.24	gold quality
skin of leg	UBERON:0001511	54.00	gold quality
tonsil	UBERON:0002372	53.88	gold quality
zone of skin	UBERON:0000014	53.78	gold quality
skin of abdomen	UBERON:0001416	53.60	gold quality
placenta	UBERON:0001987	52.81	gold quality
bone marrow cell	CL:0002092	52.64	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

61 targeting FAM72C, 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-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-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-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
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363

Literature-anchored findings (GeneRIF, showing 1)

• An epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci (FAM72A, FAM72B, FAM72C, FAM72D). (PMID:26206078)

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), FAM72D (ENSG00000215784)

Protein

Protein identifiers

Protein FAM72C — H0Y354 (reviewed: H0Y354)

All UniProt accessions (2): A0A087WSW5, H0Y354

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM72 family.

RefSeq proteins (3): NP_001274314, NP_001332999, NP_001333000 (=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-H0Y354-F1	85.51	0.66

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 37 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, chr1q21, VECCHI_GASTRIC_CANCER_EARLY_UP, CHICAS_RB1_TARGETS_GROWING, JOHNSTONE_PARVB_TARGETS_3_DN, ZWANG_DOWN_BY_2ND_EGF_PULSE, MIR1277_5P, MIR3121_3P, MIR10527_5P, MIR4482_3P, MIR206, MIR1_3P

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

520 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM72C	SRGAP2B	P0DMP2	590
FAM72C	SRGAP2C	P0DJJ0	518
FAM72C	ANKRD20A3P	Q5VUR7	518
FAM72C	ARHGAP11B	Q3KRB8	514
FAM72C	ZNG1F	Q4V339	491
FAM72C	ZNG1C	Q5JTY5	490
FAM72C	GTF2H2C	Q6P1K8	456
FAM72C	ARHGEF35	A5YM69	452
FAM72C	ZNG1A	Q9BRT8	448
FAM72C	ANKRD20A4P	Q4UJ75	447
FAM72C	ANKRD20A2P	Q5SQ80	447
FAM72C	GTF2H2	Q13888	436
FAM72C	OTUD7A	Q8TE49	432
FAM72C	CD8B2	A6NJW9	429
FAM72C	ALG1L2	C9J202	420

IntAct

0 interactions, top by confidence:

BioGRID (2): FAM72C (Negative Genetic), FAM72C (Negative Genetic)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	1
Benign	8

Top pathogenic / likely-pathogenic (0)

SpliceAI

1678 predictions. Top by Δscore:

Variant	Effect	Δscore
1:143964978:GT:G	acceptor_gain	1.0000
1:143971812:G:T	donor_gain	1.0000
1:143971814:C:A	donor_gain	1.0000
1:143971841:AGTCC:A	donor_gain	1.0000
1:143971843:G:T	donor_gain	1.0000
1:143971845:C:A	donor_gain	1.0000
1:143971857:G:GT	donor_gain	1.0000
1:143971858:T:TA	donor_gain	1.0000
1:143956478:ACACC:A	acceptor_loss	0.9900
1:143956479:CAC:C	acceptor_gain	0.9900
1:143956479:CACCT:C	acceptor_loss	0.9900
1:143956480:ACCTG:A	acceptor_loss	0.9900
1:143956481:CCT:C	acceptor_loss	0.9900
1:143956482:C:CA	acceptor_loss	0.9900
1:143956482:C:CC	acceptor_gain	0.9900
1:143956483:T:A	acceptor_loss	0.9900
1:143964849:TCTTA:T	donor_loss	0.9900
1:143964850:CTTAC:C	donor_loss	0.9900
1:143964851:TTACC:T	donor_loss	0.9900
1:143964852:TA:T	donor_loss	0.9900
1:143964853:A:AG	donor_loss	0.9900
1:143964978:G:GG	acceptor_gain	0.9900
1:143964978:GTG:G	acceptor_gain	0.9900
1:143964978:GTGG:G	acceptor_gain	0.9900
1:143964979:A:AG	acceptor_gain	0.9900
1:143964979:AGT:A	acceptor_gain	0.9900
1:143964979:AGTG:A	acceptor_gain	0.9900
1:143968997:CTGCG:C	acceptor_gain	0.9900
1:143968998:TGCGC:T	acceptor_loss	0.9900
1:143969000:CGCTG:C	acceptor_loss	0.9900

AlphaMissense

997 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:143971082:G:C	F20L	0.856
1:143971082:G:T	F20L	0.856
1:143971084:A:G	F20L	0.856
1:143971013:G:C	F43L	0.779
1:143971013:G:T	F43L	0.779
1:143971015:A:G	F43L	0.779
1:143964898:A:C	F104L	0.751
1:143964898:A:T	F104L	0.751
1:143964900:A:G	F104L	0.751
1:143971118:G:C	F8L	0.694
1:143971118:G:T	F8L	0.694
1:143971120:A:G	F8L	0.694
1:143968989:G:C	F55L	0.682
1:143968989:G:T	F55L	0.682
1:143968991:A:G	F55L	0.682
1:143971064:G:C	S26R	0.660
1:143971064:G:T	S26R	0.660
1:143971066:T:G	S26R	0.660
1:143968971:G:C	F61L	0.628
1:143968971:G:T	F61L	0.628
1:143968973:A:G	F61L	0.628
1:143964907:G:C	F101L	0.603
1:143964907:G:T	F101L	0.603
1:143964909:A:G	F101L	0.603

dbSNP variants (sampled 300 via entrez): RS10718 (1:143955516 G>A), RS1156261188 (1:143969554 T>C), RS1156324725 (1:143967935 G>A), RS1156453836 (1:143971273 G>A), RS1156715574 (1:143966331 A>T), RS1156932126 (1:143967082 C>A), RS1157213736 (1:143959977 C>A), RS1157591847 (1:143974651 A>G), RS1157619331 (1:143957595 T>C), RS1157652923 (1:143959536 A>G), RS1157683199 (1:143958203 CTCG>C), RS1157770259 (1:143972982 C>A,T), RS1157815898 (1:143975048 A>G), RS1157962614 (1:143974273 C>A,T), RS1158358905 (1:143955642 G>T)

Disease associations

OMIM: gene MIM:616853 | 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

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	1
sodium arsenite	increases expression	1
perfluorooctanoic acid	decreases expression	1
manganese chloride	increases expression, increases abundance	1
azoxystrobin	increases expression	1
fenpyroximate	increases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	increases expression	1
pyrimidifen	increases expression	1
(+)-JQ1 compound	decreases expression	1
Antimycin A	increases expression	1
Manganese	increases abundance, increases expression	1
Rotenone	increases expression	1
Tretinoin	decreases expression	1
Okadaic Acid	increases expression	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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