FAM241A

Summary

FAM241A (family with sequence similarity 241 member A, HGNC:26813) is a protein-coding gene on chromosome 4q25, encoding Uncharacterized protein FAM241A (Q8N8J7).

Located in Golgi apparatus.

Source: NCBI Gene 132720 — RefSeq curated summary.

At a glance

• GWAS associations: 22
• Clinical variants (ClinVar): 9 total — 1 pathogenic
• MANE Select transcript: NM_152400

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26813
Approved symbol	FAM241A
Name	family with sequence similarity 241 member A
Location	4q25
Locus type	gene with protein product
Status	Approved
Aliases	FLJ39370
Ensembl gene	ENSG00000174749
Ensembl biotype	protein_coding
Entrez	132720

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000309733

RefSeq mRNA: 1 — MANE Select: NM_152400 NM_152400

CCDS: CCDS3695

Canonical transcript exons

ENST00000309733 — 2 exons

Exon	Start	End
ENSE00001205163	112145454	112145733
ENSE00003994280	112186693	112195256

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 95.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.4666 / max 736.2389, expressed in 1746 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
49278	14.4532	1635
49277	6.4323	1562
49276	0.6614	424
49279	0.5620	323
49280	0.3577	181

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parietal pleura	UBERON:0002400	95.23	gold quality
heart right ventricle	UBERON:0002080	94.60	gold quality
left ventricle myocardium	UBERON:0006566	94.33	gold quality
skin of hip	UBERON:0001554	93.66	gold quality
visceral pleura	UBERON:0002401	93.40	gold quality
myocardium	UBERON:0002349	92.63	gold quality
epithelial cell of pancreas	CL:0000083	92.41	gold quality
cardiac muscle of right atrium	UBERON:0003379	92.11	gold quality
upper leg skin	UBERON:0004262	90.91	gold quality
parotid gland	UBERON:0001831	90.67	gold quality
epithelium of mammary gland	UBERON:0003244	90.59	gold quality
mammary duct	UBERON:0001765	90.53	gold quality
thoracic mammary gland	UBERON:0005200	90.30	gold quality
mammary gland	UBERON:0001911	90.20	gold quality
pericardium	UBERON:0002407	88.95	gold quality
adipose tissue	UBERON:0001013	87.66	gold quality
upper arm skin	UBERON:0004263	87.45	gold quality
tibia	UBERON:0000979	86.98	gold quality
esophagus squamous epithelium	UBERON:0006920	86.76	gold quality
tibialis anterior	UBERON:0001385	86.66	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	86.56	gold quality
trabecular bone tissue	UBERON:0002483	86.41	gold quality
seminal vesicle	UBERON:0000998	86.28	gold quality
biceps brachii	UBERON:0001507	85.89	gold quality
adipose tissue of abdominal region	UBERON:0007808	85.76	gold quality
oral cavity	UBERON:0000167	85.73	gold quality
omental fat pad	UBERON:0010414	85.16	gold quality
peritoneum	UBERON:0002358	85.09	gold quality
subcutaneous adipose tissue	UBERON:0002190	84.86	gold quality
deltoid	UBERON:0001476	84.30	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-6819	yes	1052.03
E-ANND-3	yes	17.57
E-MTAB-9067	yes	6.52
E-CURD-112	yes	5.03
E-GEOD-150728	no	2241.91
E-MTAB-6678	no	2197.67
E-ENAD-27	no	324.60
E-MTAB-7249	no	316.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

141 targeting FAM241A, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488

Literature-anchored findings (GeneRIF, showing 1)

• Data indicate associations of SNPs in eight loci CXCR4, HHEX, FOXA2, NGN3, TCF7L2, FLJ39370 (C4orf32), LOC646279 (RPL21P7) and THADA with body mass index (BMI) and weight. (PMID:23349771)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam241a	ENSDARG00000057006
mus_musculus	Fam241a	ENSMUSG00000050549
rattus_norvegicus	Fam241a	ENSRNOG00000010875

Paralogs (1): FAM241B (ENSG00000171224)

Protein

Protein identifiers

Uncharacterized protein FAM241A — Q8N8J7 (reviewed: Q8N8J7)

All UniProt accessions (1): Q8N8J7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the FAM241 family.

RefSeq proteins (1): NP_689613* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027953	DUF4605	Domain
IPR052502	FAM241_domain	Family

Pfam: PF15378

UniProt features (6 total): sequence conflict 2, chain 1, transmembrane region 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N8J7-F1	58.47	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 175 (showing top): chr4q25, GOZGIT_ESR1_TARGETS_DN, NFKB_C, FOSTER_TOLERANT_MACROPHAGE_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, COATES_MACROPHAGE_M1_VS_M2_DN, HAND1E47_01, CUI_TCF21_TARGETS_2_DN, DELASERNA_MYOD_TARGETS_UP, RGAGGAARY_PU1_Q6, TGGAAA_NFAT_Q4_01, NUYTTEN_EZH2_TARGETS_DN, LEE_RECENT_THYMIC_EMIGRANT, GEORGES_TARGETS_OF_MIR192_AND_MIR215, KIM_MYCN_AMPLIFICATION_TARGETS_UP

GO Biological Process (0):

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

GO Cellular Component (2): Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM241A	AGAP5	A6NIR3	521
FAM241A	PKN2	Q16513	472
FAM241A	CDKAL1	Q5VV42	436
FAM241A	PRSS36	Q5K4E3	407
FAM241A	HHEX	Q03014	400
FAM241A	DIPK1C	Q0P6D2	376
FAM241A	SAPCD1	Q5SSQ6	373
FAM241A	SLC30A8	Q8IWU4	373
FAM241A	KLHL3	Q9UH77	370
FAM241A	SMIM14	Q96QK8	359
FAM241A	PRSS53	Q2L4Q9	327
FAM241A	CEACAM19	Q7Z692	324
FAM241A	ZNF668	Q96K58	321
FAM241A	RELL1	Q8IUW5	320
FAM241A	ENPEP	Q07075	317

IntAct

88 interactions, top by confidence:

A	B	Type	Score
CD27	TCAF2	psi-mi:“MI:0914”(association)	0.640
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
STT3A	RPN1	psi-mi:“MI:0914”(association)	0.560
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
IPPK	TMEM223	psi-mi:“MI:0914”(association)	0.530
C3AR1	TMEM120B	psi-mi:“MI:0914”(association)	0.530
FZD10	NRP1	psi-mi:“MI:0914”(association)	0.530
REEP5	SCAMP1	psi-mi:“MI:0914”(association)	0.530
ZACN	GPAA1	psi-mi:“MI:0914”(association)	0.530
TSPAN2	TSPAN3	psi-mi:“MI:0914”(association)	0.530
RPN2	SMPD2	psi-mi:“MI:0914”(association)	0.530
ZDHHC11	APOB	psi-mi:“MI:0914”(association)	0.530
RPN1	APBB1	psi-mi:“MI:0914”(association)	0.530
FAM241A	NRP1	psi-mi:“MI:0914”(association)	0.530
MFSD8	FAM241A	psi-mi:“MI:0914”(association)	0.530
CD40	EXOC5	psi-mi:“MI:0914”(association)	0.530
FAM241A	SPTLC2	psi-mi:“MI:0914”(association)	0.530
REEP5	PLSCR1	psi-mi:“MI:0914”(association)	0.530
LINGO1	LGALS8	psi-mi:“MI:0914”(association)	0.530
CLEC10A	FAM241A	psi-mi:“MI:0915”(physical association)	0.500
ORF28	PEX19	psi-mi:“MI:0914”(association)	0.350
RTN1	TMEM120B	psi-mi:“MI:0914”(association)	0.350
VIPR2	C15orf61	psi-mi:“MI:0914”(association)	0.350
FPR2	GPR89A	psi-mi:“MI:0914”(association)	0.350

BioGRID (145): C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS)

ESM2 similar proteins: A4Q9F3, A8IHN8, D3YYI7, M0R7T9, O09112, O60347, O88751, P51509, Q09YL6, Q0IHH1, Q13202, Q13505, Q14190, Q147X3, Q17QD9, Q3TZ87, Q3UPL5, Q3V1H9, Q5TGI4, Q5VUJ9, Q5VV17, Q5XI57, Q61079, Q6A039, Q6PDS0, Q6ZVT0, Q7Z7K6, Q80UW0, Q86YJ5, Q8C4U2, Q8CES0, Q8N554, Q8N8J7, Q8TC41, Q8TDR2, Q8WWW0, Q96AQ8, Q96ET8, Q96KN8, Q96MM7

Diamond homologs: Q17QE0, Q8N8J7, Q9CZL2, Q9D882, Q96D05

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 111 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
PD-L1(CD274) glycosylation and translocation to plasma membrane	6	47.2×	7e-07
Regulation of CDH1 posttranslational processing and trafficking to plasma membrane	6	30.5×	4e-06
Maturation of spike protein	7	28.2×	7e-07
Maturation of DENV proteins	6	19.2×	5e-05

GO biological processes:

GO term	Partners	Fold	FDR
obsolete protein N-linked glycosylation via asparagine	5	34.0×	1e-04
protein N-linked glycosylation	6	16.0×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
980126	GRCh37/hg19 4q25(chr4:111334313-113223858)x1	Pathogenic

SpliceAI

659 predictions. Top by Δscore:

Variant	Effect	Δscore
4:112180854:GAACT:G	donor_gain	1.0000
4:112186688:TAAAG:T	acceptor_loss	1.0000
4:112186689:A:AG	acceptor_gain	1.0000
4:112186689:AAAG:A	acceptor_gain	1.0000
4:112186690:A:G	acceptor_gain	1.0000
4:112186690:AAG:A	acceptor_gain	1.0000
4:112186691:AG:A	acceptor_gain	1.0000
4:112186692:G:C	acceptor_loss	1.0000
4:112186692:GG:G	acceptor_gain	1.0000
4:112186692:GGAT:G	acceptor_gain	1.0000
4:112186806:G:GT	donor_gain	1.0000
4:112186837:G:GG	donor_gain	1.0000
4:112145730:GCAG:G	donor_gain	0.9900
4:112171370:C:G	donor_gain	0.9900
4:112180785:G:GG	donor_gain	0.9900
4:112180815:G:GT	donor_gain	0.9900
4:112180859:G:GG	donor_gain	0.9900
4:112186691:A:G	acceptor_gain	0.9900
4:112186691:AGGAT:A	acceptor_gain	0.9900
4:112186692:G:GC	acceptor_gain	0.9900
4:112186692:GGATG:G	acceptor_gain	0.9900
4:112186806:G:T	donor_gain	0.9900
4:112145723:A:T	donor_gain	0.9800
4:112145731:CAGG:C	donor_loss	0.9800
4:112145732:AGGT:A	donor_loss	0.9800
4:112145733:GGTGA:G	donor_loss	0.9800
4:112145735:T:G	donor_loss	0.9800
4:112180672:A:AG	acceptor_gain	0.9800
4:112180673:G:GG	acceptor_gain	0.9800
4:112180673:GTCA:G	acceptor_gain	0.9800

AlphaMissense

853 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:112186909:T:C	C124R	0.991
4:112186907:T:A	L123H	0.990
4:112186798:T:C	F87L	0.988
4:112186799:T:C	F87S	0.988
4:112186800:C:A	F87L	0.988
4:112186800:C:G	F87L	0.988
4:112186784:T:C	L82P	0.987
4:112186784:T:A	L82H	0.984
4:112186855:T:A	W106R	0.983
4:112186855:T:C	W106R	0.983
4:112186876:G:C	G113R	0.982
4:112186891:G:A	G118R	0.981
4:112186891:G:C	G118R	0.981
4:112186775:A:T	N79I	0.979
4:112186776:C:A	N79K	0.979
4:112186776:C:G	N79K	0.979
4:112186895:T:C	L119P	0.979
4:112186762:T:C	F75L	0.978
4:112186764:T:A	F75L	0.978
4:112186764:T:G	F75L	0.978
4:112186835:C:A	P99Q	0.978
4:112186835:C:G	P99R	0.976
4:112186870:T:C	F111L	0.976
4:112186872:C:A	F111L	0.976
4:112186872:C:G	F111L	0.976
4:112186901:C:A	A121D	0.976
4:112186907:T:G	L123R	0.976
4:112186867:T:A	W110R	0.974
4:112186867:T:C	W110R	0.974
4:112186862:T:G	M108R	0.973

dbSNP variants (sampled 300 via entrez): RS1000043603 (4:112145002 G>C), RS1000054592 (4:112145154 ACTCT>A,ACT), RS1000108840 (4:112151982 T>A), RS1000131133 (4:112158722 A>G), RS10002700 (4:112145675 G>A,C), RS1000445752 (4:112174873 T>C,G), RS1000456771 (4:112188953 T>A), RS1000500624 (4:112187802 T>C), RS1000524148 (4:112171312 C>A,T), RS1000627423 (4:112169588 T>C), RS1000628801 (4:112183288 TAAAAAA>T,TAAAAA,TAAAAAAA), RS1000699474 (4:112184433 G>A), RS1000835313 (4:112184123 C>T), RS1000865767 (4:112164071 C>A), RS1001045486 (4:112146586 C>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

22 associations (top):

Study	Trait	p-value
GCST003992_34	Photic sneeze reflex	3.000000e-31
GCST005170_49	Intraocular pressure	3.000000e-10
GCST005951_145	Body mass index	4.000000e-08
GCST006061_122	Atrial fibrillation	7.000000e-71
GCST006061_129	Atrial fibrillation	2.000000e-39
GCST006061_133	Atrial fibrillation	8.000000e-12
GCST006061_145	Atrial fibrillation	1.000000e-15
GCST006061_152	Atrial fibrillation	6.000000e-09
GCST006061_153	Atrial fibrillation	0.000000e+00
GCST006061_21	Atrial fibrillation	6.000000e-113
GCST006061_38	Atrial fibrillation	0.000000e+00
GCST006061_39	Atrial fibrillation	0.000000e+00
GCST006061_66	Atrial fibrillation	0.000000e+00
GCST007327_101	Smoking status (ever vs never smokers)	3.000000e-10
GCST008667_1	Smoking status (heavy vs never)	5.000000e-08
GCST009462_30	Optic disc size	2.000000e-13
GCST009541_2	Heart failure	6.000000e-20
GCST009597_40	Multiple sclerosis	2.000000e-07
GCST010988_234	Adult body size	3.000000e-08
GCST90002388_353	Lymphocyte count	1.000000e-25
GCST90002389_195	Lymphocyte percentage of white cells	3.000000e-21
GCST90002399_383	Neutrophil percentage of white cells	1.000000e-16

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0007887	autosomal dominant compelling helio-ophthalmic outburst syndrome
EFO:0004695	intraocular pressure measurement
EFO:0004340	body mass index
EFO:0004318	smoking behavior
EFO:0006527	smoking status measurement
EFO:0004587	lymphocyte count
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0007990	neutrophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

63 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, affects cotreatment, increases expression	9
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	4
Cyclosporine	increases expression	4
Benzo(a)pyrene	affects methylation, increases expression	3
methylmercuric chloride	decreases expression	2
trichostatin A	affects expression, increases expression	2
entinostat	increases expression, affects cotreatment	2
Acetaminophen	increases expression	2
Air Pollutants	increases abundance, increases expression, decreases expression	2
Dexamethasone	increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tretinoin	decreases expression, increases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, increases expression	1
sotorasib	affects cotreatment, decreases expression	1
bisphenol A	affects cotreatment, increases expression	1
kojic acid	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
perfluorooctanoic acid	increases expression	1
resorcinol	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
mercuric bromide	affects cotreatment, increases expression	1
avobenzone	decreases expression	1
Am 580	decreases expression	1
perfluoro-n-nonanoic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
2,2’,4,4’,5-brominated diphenyl ether	increases expression	1

Clinical trials (associated diseases)

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