FAM25C

Summary

FAM25C (family with sequence similarity 25 member C, HGNC:23586) is a protein-coding gene on chromosome 10q11.22, encoding Protein FAM25C (B3EWG5).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 23 total — 1 likely-pathogenic
• MANE Select transcript: NM_001137548

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23586
Approved symbol	FAM25C
Name	family with sequence similarity 25 member C
Location	10q11.22
Locus type	gene with protein product
Status	Approved
Aliases	bA164N7.4
Ensembl gene	ENSG00000276430
Ensembl biotype	protein_coding
Entrez	644054

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000617224

RefSeq mRNA: 1 — MANE Select: NM_001137548 NM_001137548

CCDS: CCDS76299

Canonical transcript exons

ENST00000617224 — 3 exons

Exon	Start	End
ENSE00002460234	47997677	47997739
ENSE00003738279	47999693	47999791
ENSE00003756655	47995322	47995511

Expression profiles

Bgee: expression breadth broad, 58 present calls, max score 90.10.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	90.10	gold quality
zone of skin	UBERON:0000014	88.68	gold quality
skin of abdomen	UBERON:0001416	88.50	gold quality
lower esophagus mucosa	UBERON:0035834	81.50	gold quality
esophagus mucosa	UBERON:0002469	71.66	gold quality
vagina	UBERON:0000996	52.76	gold quality
esophagus	UBERON:0001043	46.63	gold quality
tonsil	UBERON:0002372	42.62	gold quality
ectocervix	UBERON:0012249	37.98	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
minor salivary gland	UBERON:0001830	34.05	gold quality
saliva-secreting gland	UBERON:0001044	33.61	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
small intestine	UBERON:0002108	33.29	gold quality
small intestine Peyer’s patch	UBERON:0003454	32.96	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
uterine cervix	UBERON:0000002	31.22	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
multicellular organism	UBERON:0000468	29.07	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
blood	UBERON:0000178	26.95	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.97

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam25a	ENSMUSG00000043681
rattus_norvegicus	Fam25a	ENSRNOG00000055025

Paralogs (2): FAM25A (ENSG00000188100), FAM25G (ENSG00000189090)

Protein

Protein identifiers

Protein FAM25C — B3EWG5 (reviewed: B3EWG5)

All UniProt accessions (1): B3EWG5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM25 family.

RefSeq proteins (1): NP_001131020* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR023243	FAM25	Family

Pfam: PF15825

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B3EWG5-F1	59.12	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 7 (showing top): GSE2405_0H_VS_1.5H_A_PHAGOCYTOPHILUM_STIM_NEUTROPHIL_UP, GSE5589_WT_VS_IL10_KO_LPS_AND_IL6_STIM_MACROPHAGE_45MIN_UP, GSE19888_CTRL_VS_T_CELL_MEMBRANES_ACT_MAST_CELL_DN, chr10q11, GSE16385_MONOCYTE_VS_12H_IFNG_TNF_TREATED_MACROPHAGE_DN, GSE11961_GERMINAL_CENTER_BCELL_DAY7_VS_PLASMA_CELL_DAY7_UP, GSE41176_UNSTIM_VS_ANTI_IGM_STIM_BCELL_24H_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

BioGRID (62): FAM25A (Two-hybrid), FAM25G (Two-hybrid), FAM25C (Two-hybrid), FAM25A (Two-hybrid), FAM25G (Two-hybrid), FAM25C (Two-hybrid), FAM25A (Two-hybrid), FAM25G (Two-hybrid), FAM25C (Two-hybrid), FAM25A (Two-hybrid), FAM25G (Two-hybrid), FAM25C (Two-hybrid), FAM25A (Two-hybrid), FAM25G (Two-hybrid), FAM25C (Two-hybrid)

ESM2 similar proteins: A0A0C4G489, A0A6B9KZ02, A0A6B9L6A5, B3EWG3, B3EWG5, B3EWG6, B4II55, B4PPU6, B9WG30, C0HJX8, D6C4I6, F1T149, F1T150, L0GCW2, O18493, O31557, O96059, O97395, P0DM82, P0DP51, P0DPH1, P0DPH5, P0DQV6, P0DTG2, P0DUE8, P10762, P13404, P21663, P40844, P53707, P80710, P80713, P81605, P82818, P85219, P85222, P86718, P86719, Q07730, Q1JS87

Diamond homologs: B3EWG3, B3EWG5, B3EWG6, Q8CF02

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	20
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
495230	NC_000010.10:g.43611191_61663279inv	Likely pathogenic

SpliceAI

358 predictions. Top by Δscore:

Variant	Effect	Δscore
10:47995507:AATGG:A	acceptor_gain	1.0000
10:47995508:ATGG:A	acceptor_gain	1.0000
10:47995509:TGG:T	acceptor_gain	1.0000
10:47995512:C:CC	acceptor_gain	1.0000
10:47995515:T:TC	acceptor_gain	1.0000
10:47997740:C:CC	acceptor_gain	1.0000
10:47999686:T:TA	donor_gain	1.0000
10:47999691:A:AC	donor_gain	1.0000
10:47999692:C:CC	donor_gain	1.0000
10:47999692:CTGG:C	donor_gain	1.0000
10:47999698:C:CA	donor_gain	1.0000
10:47995509:TGGC:T	acceptor_loss	0.9900
10:47995510:GG:G	acceptor_gain	0.9900
10:47995510:GGC:G	acceptor_loss	0.9900
10:47995511:GCT:G	acceptor_loss	0.9900
10:47995512:C:A	acceptor_loss	0.9900
10:47995515:T:C	acceptor_gain	0.9900
10:47997671:CTGTA:C	donor_loss	0.9900
10:47997672:TGTA:T	donor_loss	0.9900
10:47997674:TA:T	donor_loss	0.9900
10:47997676:C:CG	donor_loss	0.9900
10:47997736:TGAA:T	acceptor_gain	0.9900
10:47997737:GAA:G	acceptor_gain	0.9900
10:47997738:AAC:A	acceptor_loss	0.9900
10:47997740:C:CA	acceptor_loss	0.9900
10:47997745:C:CT	acceptor_gain	0.9900
10:47997735:ATGAA:A	acceptor_gain	0.9800
10:47997746:A:T	acceptor_gain	0.9800
10:47999687:CCTCA:C	donor_loss	0.9800
10:47999688:CTCAC:C	donor_loss	0.9800

AlphaMissense

568 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS11100980 (10:47998213 G>C,T), RS11101443 (10:47994914 A>T), RS113501518 (10:47996579 G>A), RS113729642 (10:48001623 G>A,T), RS1156458556 (10:47996571 G>A), RS1156650567 (10:47999105 C>T), RS1156671234 (10:47998455 G>A), RS1157294910 (10:47999888 C>T), RS1157608858 (10:48001479 C>A,T), RS1157826138 (10:47996848 TTG>T), RS1158159400 (10:47997360 C>A,T), RS1158170581 (10:47996047 T>G), RS1158850781 (10:47999576 C>T), RS1159099812 (10:47998734 C>T), RS1159374027 (10:47996853 A>G,T)

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

1 associations (top):

Study	Trait	p-value
GCST90016675_6	Pancreas fat	2.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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