FAM25A

Summary

FAM25A (family with sequence similarity 25 member A, HGNC:23436) is a protein-coding gene on chromosome 10q23.2, encoding Protein FAM25A (B3EWG3).

At a glance

• Clinical variants (ClinVar): 13 total
• MANE Select transcript: NM_001146157

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23436
Approved symbol	FAM25A
Name	family with sequence similarity 25 member A
Location	10q23.2
Locus type	gene with protein product
Status	Approved
Aliases	bA96C23.5
Ensembl gene	ENSG00000188100
Ensembl biotype	protein_coding
Entrez	643161

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000343959

RefSeq mRNA: 1 — MANE Select: NM_001146157 NM_001146157

CCDS: CCDS44451

Canonical transcript exons

ENST00000343959 — 3 exons

Exon	Start	End
ENSE00002449898	87020294	87020397
ENSE00003291911	87024541	87024730
ENSE00003472883	87022314	87022376

Expression profiles

Bgee: expression breadth ubiquitous, 102 present calls, max score 99.13.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4997 / max 78.4378, expressed in 117 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
106012	0.4997	117

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	99.13	gold quality
skin of leg	UBERON:0001511	95.39	gold quality
zone of skin	UBERON:0000014	95.34	gold quality
skin of abdomen	UBERON:0001416	95.19	gold quality
esophagus mucosa	UBERON:0002469	92.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.15	gold quality
vagina	UBERON:0000996	73.49	gold quality
esophagus	UBERON:0001043	66.95	gold quality
right adrenal gland	UBERON:0001233	62.83	gold quality
tonsil	UBERON:0002372	59.69	gold quality
right adrenal gland cortex	UBERON:0035827	58.58	gold quality
left adrenal gland cortex	UBERON:0035825	58.01	gold quality
left adrenal gland	UBERON:0001234	56.50	gold quality
apex of heart	UBERON:0002098	56.14	gold quality
minor salivary gland	UBERON:0001830	54.75	gold quality
saliva-secreting gland	UBERON:0001044	52.47	gold quality
adrenal gland	UBERON:0002369	52.45	gold quality
placenta	UBERON:0001987	50.20	gold quality
mucosa of stomach	UBERON:0001199	45.32	gold quality
uterine cervix	UBERON:0000002	44.82	gold quality
ectocervix	UBERON:0012249	43.36	gold quality
colonic epithelium	UBERON:0000397	42.79	gold quality
sural nerve	UBERON:0015488	40.92	gold quality
bone marrow cell	CL:0002092	39.50	silver quality
lower esophagus	UBERON:0013473	38.40	gold quality
lower esophagus muscularis layer	UBERON:0035833	38.30	gold quality
multicellular organism	UBERON:0000468	37.53	gold quality
skeletal muscle tissue	UBERON:0001134	37.15	gold quality
right lobe of liver	UBERON:0001114	36.55	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.57

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam25a	ENSMUSG00000043681
rattus_norvegicus	Fam25a	ENSRNOG00000055025

Paralogs (2): FAM25G (ENSG00000189090), FAM25C (ENSG00000276430)

Protein

Protein identifiers

Protein FAM25A — B3EWG3 (reviewed: B3EWG3)

All UniProt accessions (1): B3EWG3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM25 family.

RefSeq proteins (1): NP_001139629* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR023243	FAM25	Family

Pfam: PF15825

UniProt features (2 total): chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B3EWG3-F1	61.17	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 13 (showing top): YAMAZAKI_TCEB3_TARGETS_DN, chr10q23, MIKKELSEN_IPS_LCP_WITH_H3K4ME3, MIKKELSEN_ES_LCP_WITH_H3K4ME3, LU_EZH2_TARGETS_UP, DELACROIX_RAR_BOUND_ES, FORTSCHEGGER_PHF8_TARGETS_DN, FOSTER_KDM1A_TARGETS_UP, BLANCO_MELO_BETA_INTERFERON_TREATED_BRONCHIAL_EPITHELIAL_CELLS_DN, ZAK_PBMC_MRKAD5_HIV_1_GAG_POL_NEF_AGE_20_50YO_AD5_NAB_TITERS_GT_200_VS_LTE_200_1DY_DN, HE_LIM_SUN_FETAL_LUNG_C1_SQUAMOUS_CELL, MA_RAT_AGING_DN, WP_10Q22Q23_COPY_NUMBER_VARIATION

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

196 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM25A	ANTXRL	A6NF34	595
FAM25A	NUTM2D	Q5VT03	528
FAM25A	A0A087WTP8	A0A087WTP8	519
FAM25A	AGAP6	Q5VW22	480
FAM25A	NPIPB9	F8W1W9	479
FAM25A	MMRN2	Q9H8L6	468
FAM25A	MTRNR2L10	P0CJ77	446
FAM25A	CRCT1	Q9UGL9	418
FAM25A	GTSF1L	Q9H1H1	400
FAM25A	ASAH2B	P0C7U1	399
FAM25A	TMEM273	Q5T292	399
FAM25A	LRRC18	Q8N456	396
FAM25A	B3GNT9	Q6UX72	392
FAM25A	FRMPD2	Q68DX3	377
FAM25A	RGPD5	Q99666	372
FAM25A	Q8WV35	Q8WV35	372

IntAct

58 interactions, top by confidence:

A	B	Type	Score
SNX1	FAM25C	psi-mi:“MI:0915”(physical association)	0.560
COX16	FAM25C	psi-mi:“MI:0915”(physical association)	0.560
ZFAND3	FAM25C	psi-mi:“MI:0915”(physical association)	0.560
IGLL1	FAM25C	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	ARMC10	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	S100A6	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	TOMM20L	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	MIEF1	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	TDRKH	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	ARMCX3	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	TTPA	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	LCN1	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	PPIF	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	PPIC	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	SNX1	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	COX16	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	MIEF2	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	ZFAND3	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	GPD1	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	IGLL1	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	KLHL35	psi-mi:“MI:0915”(physical association)	0.560
FAM25C	LCN2	psi-mi:“MI:0915”(physical association)	0.560
CCR1	UBA6	psi-mi:“MI:0914”(association)	0.350
ARMC10	FAM25C	psi-mi:“MI:0915”(physical association)	0.000
ARMCX3	FAM25C	psi-mi:“MI:0915”(physical association)	0.000

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

233 predictions. Top by Δscore:

Variant	Effect	Δscore
10:87020391:G:GT	donor_gain	1.0000
10:87020394:GCCA:G	donor_gain	1.0000
10:87020398:G:GG	donor_gain	1.0000
10:87020403:G:GT	donor_gain	1.0000
10:87022312:A:AG	acceptor_gain	1.0000
10:87022313:G:GG	acceptor_gain	1.0000
10:87022373:AAAG:A	donor_loss	1.0000
10:87022374:AAGG:A	donor_loss	1.0000
10:87022375:AGG:A	donor_loss	1.0000
10:87022376:GG:G	donor_loss	1.0000
10:87022307:T:A	acceptor_gain	0.9900
10:87022311:CA:C	acceptor_loss	0.9900
10:87022312:A:AC	acceptor_loss	0.9900
10:87022313:G:GT	acceptor_loss	0.9900
10:87022313:GTT:G	acceptor_gain	0.9900
10:87022313:GTTC:G	acceptor_gain	0.9900
10:87022372:GAAAG:G	donor_gain	0.9900
10:87024536:A:AG	acceptor_gain	0.9900
10:87024537:A:G	acceptor_gain	0.9900
10:87024537:ACAGC:A	acceptor_loss	0.9900
10:87024539:A:AG	acceptor_gain	0.9900
10:87024539:AGCC:A	acceptor_loss	0.9900
10:87024540:G:GG	acceptor_gain	0.9900
10:87024540:GC:G	acceptor_gain	0.9900
10:87024540:GCC:G	acceptor_gain	0.9900
10:87024540:GCCA:G	acceptor_gain	0.9900
10:87024540:GCCAT:G	acceptor_gain	0.9900
10:87022313:GT:G	acceptor_gain	0.9800
10:87022313:GTTCA:G	acceptor_gain	0.9800
10:87020378:G:GT	donor_gain	0.9700

AlphaMissense

568 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:87020350:C:A	A9D	0.895
10:87020352:G:C	A10P	0.865
10:87020340:G:T	G6W	0.851
10:87020371:G:C	R16P	0.829
10:87024622:T:A	V73D	0.823
10:87020358:G:C	G12R	0.799
10:87020340:G:A	G6R	0.796
10:87020340:G:C	G6R	0.796
10:87020382:G:C	A20P	0.796
10:87024630:G:C	A76P	0.783
10:87022355:G:C	A39P	0.780
10:87022356:C:A	A39D	0.754
10:87022335:T:A	V32E	0.749
10:87020364:G:C	A14P	0.743
10:87020365:C:A	A14D	0.741
10:87020331:G:A	G3R	0.737
10:87020331:G:C	G3R	0.737
10:87020341:G:T	G6V	0.737
10:87020349:G:C	A9P	0.736
10:87020374:C:T	T17I	0.735
10:87024552:G:C	A50P	0.732
10:87020386:C:T	T21I	0.722
10:87020370:C:A	R16S	0.693
10:87020347:T:C	L8P	0.689
10:87024564:G:C	A54P	0.689
10:87024610:T:A	V69E	0.686
10:87020362:T:C	L13P	0.685
10:87022360:G:C	K40N	0.684
10:87022360:G:T	K40N	0.684
10:87022323:T:A	V28E	0.678

dbSNP variants (sampled 300 via entrez): RS1000007170 (10:87020525 C>T), RS1000080450 (10:87020354 C>A,T), RS1001686919 (10:87021946 G>A), RS1002019008 (10:87023568 A>T), RS1002094049 (10:87023220 C>A,T), RS1002927767 (10:87019110 A>G), RS1003696672 (10:87024979 G>GA), RS1004573858 (10:87018514 A>T), RS1004665217 (10:87023184 G>A), RS1004793390 (10:87018842 A>G), RS1006166026 (10:87024239 A>G), RS1006470063 (10:87020021 C>G), RS1006734759 (10:87023186 A>C), RS1006806494 (10:87021331 T>C), RS1006998012 (10:87020969 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

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
Arsenic	affects methylation, decreases expression, increases abundance	3
propionaldehyde	increases expression	1
sodium arsenate	decreases expression, increases abundance	1
beta-lapachone	increases expression	1
sodium arsenite	decreases expression, increases abundance	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Silicon Dioxide	increases expression	1
Gold Compounds	increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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