FAM241B

Summary

FAM241B (family with sequence similarity 241 member B, HGNC:23519) is a protein-coding gene on chromosome 10q22.1, encoding Protein FAM241B (Q96D05). May play a role in lysosome homeostasis.

Predicted to be located in membrane. Predicted to be active in intracellular membrane-bounded organelle.

Source: NCBI Gene 219738 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_145306

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23519
Approved symbol	FAM241B
Name	family with sequence similarity 241 member B
Location	10q22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000171224
Ensembl biotype	protein_coding
Entrez	219738

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 18 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000373279, ENST00000421716, ENST00000491890, ENST00000898846, ENST00000898847, ENST00000898848, ENST00000922481, ENST00000922482, ENST00000922483, ENST00000922484, ENST00000922485, ENST00000922486, ENST00000922487, ENST00000922488, ENST00000922489, ENST00000922490, ENST00000922491, ENST00000922492, ENST00000960616

RefSeq mRNA: 1 — MANE Select: NM_145306 NM_145306

CCDS: CCDS7295

Canonical transcript exons

ENST00000373279 — 4 exons

Exon	Start	End
ENSE00001836282	69632790	69633596
ENSE00001905421	69630247	69630313
ENSE00003477843	69631480	69631547
ENSE00003565632	69631709	69631839

Expression profiles

Bgee: expression breadth ubiquitous, 189 present calls, max score 95.93.

FANTOM5 (CAGE): breadth broad, TPM avg 2.3073 / max 32.6852, expressed in 882 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
105356	2.3073	882

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	95.93	gold quality
cerebellar cortex	UBERON:0002129	95.89	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.88	gold quality
cerebellum	UBERON:0002037	95.47	gold quality
cerebellar vermis	UBERON:0004720	94.86	gold quality
sperm	CL:0000019	94.67	gold quality
prefrontal cortex	UBERON:0000451	92.63	gold quality
right frontal lobe	UBERON:0002810	92.43	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.43	gold quality
pons	UBERON:0000988	92.11	gold quality
endothelial cell	CL:0000115	91.92	silver quality
anterior cingulate cortex	UBERON:0009835	91.77	gold quality
cortical plate	UBERON:0005343	91.52	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.14	gold quality
hypothalamus	UBERON:0001898	91.05	gold quality
middle temporal gyrus	UBERON:0002771	91.03	gold quality
frontal cortex	UBERON:0001870	90.61	gold quality
neocortex	UBERON:0001950	90.54	gold quality
cerebral cortex	UBERON:0000956	89.10	gold quality
nucleus accumbens	UBERON:0001882	88.95	gold quality
secondary oocyte	CL:0000655	88.85	gold quality
amygdala	UBERON:0001876	88.24	gold quality
brain	UBERON:0000955	88.10	gold quality
oocyte	CL:0000023	87.87	gold quality
forebrain	UBERON:0001890	87.37	gold quality
ganglionic eminence	UBERON:0004023	87.14	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.71	gold quality
primary visual cortex	UBERON:0002436	86.65	gold quality
superior vestibular nucleus	UBERON:0007227	86.36	gold quality
Ammon’s horn	UBERON:0001954	86.27	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting FAM241B, 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-95-5P	99.89	72.17	3973
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-370-5P	99.78	66.81	706
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-5009-3P	99.45	69.43	1341
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-6512-5P	98.76	69.29	1195
HSA-MIR-4662A-5P	98.48	67.18	1007
HSA-MIR-5691	98.23	67.02	1335
HSA-MIR-6805-3P	98.23	67.02	1334
HSA-MIR-676-3P	97.86	65.70	668
HSA-MIR-1227-3P	97.36	66.94	834
HSA-MIR-7106-3P	97.33	65.33	644
HSA-MIR-3974	96.56	66.22	928
HSA-MIR-2276-5P	96.27	65.85	937
HSA-MIR-4315	94.78	64.86	112
HSA-MIR-6795-3P	91.86	63.00	218
HSA-MIR-4304	90.01	61.07	99

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam241b	ENSMUSG00000020083
rattus_norvegicus	Fam241b	ENSRNOG00000000551
rattus_norvegicus	Fam241b-ps1	ENSRNOG00000051000

Paralogs (1): FAM241A (ENSG00000174749)

Protein

Protein identifiers

Protein FAM241B — Q96D05 (reviewed: Q96D05)

All UniProt accessions (2): Q96D05, Q5VVH9

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in lysosome homeostasis.

Subcellular location. Membrane.

Similarity. Belongs to the FAM241 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96D05-1	1	yes
Q96D05-2	2

RefSeq proteins (1): NP_660349* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027953	DUF4605	Domain
IPR052502	FAM241_domain	Family

Pfam: PF15378

UniProt features (8 total): compositionally biased region 2, modified residue 2, chain 1, transmembrane region 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96D05-F1	65.99	0.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 33, 62

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 88 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, PATIL_LIVER_CANCER, YGACNNYACAR_UNKNOWN, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, RYTTCCTG_ETS2_B, RGAGGAARY_PU1_Q6, LEE_TARGETS_OF_PTCH1_AND_SUFU_DN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, GOTTWEIN_TARGETS_OF_KSHV_MIR_K12_11, MEISSNER_NPC_HCP_WITH_H3K4ME2, MARTENS_TRETINOIN_RESPONSE_UP, BRUINS_UVC_RESPONSE_LATE, ESC_J1_UP_EARLY.V1_UP, HOXB4_TARGET_GENES, KLF7_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

322 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM241B	E5RHQ9	E5RHQ9	527
FAM241B	TEX26	Q8N6G2	506
FAM241B	PLSCR5	A0PG75	476
FAM241B	FAM149B1	Q96BN6	448
FAM241B	FHIP1B	Q8N612	446
FAM241B	ZNF710	Q8N1W2	416
FAM241B	PLPPR2	Q96GM1	400
FAM241B	HHATL	Q9HCP6	392
FAM241B	ALKBH6	Q3KRA9	375
FAM241B	MAPRE3	Q9UPY8	367
FAM241B	IGSF9	Q9P2J2	364
FAM241B	HIRIP3	Q9BW71	360
FAM241B	TMCC2	O75069	356
FAM241B	TMIGD1	Q6UXZ0	349
FAM241B	OTOP2	Q7RTS6	349

IntAct

97 interactions, top by confidence:

A	B	Type	Score
ATP6V0C	ATP6AP2	psi-mi:“MI:0914”(association)	0.730
SYNE4	FAM241B	psi-mi:“MI:0915”(physical association)	0.560
FAM241B	SYNE4	psi-mi:“MI:0915”(physical association)	0.560
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
IPPK	TMEM223	psi-mi:“MI:0914”(association)	0.530
HTR2C	KLRG2	psi-mi:“MI:0914”(association)	0.530
MAS1	POTEF	psi-mi:“MI:0914”(association)	0.530
GABRE	FZD6	psi-mi:“MI:0914”(association)	0.530
FSHR	UPK3BL1	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
LPAR1	TMEM120B	psi-mi:“MI:0914”(association)	0.530
FAM241A	NRP1	psi-mi:“MI:0914”(association)	0.530
CD63	LGALS8	psi-mi:“MI:0914”(association)	0.530
APLNR	SLC33A1	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
WLS	FAM241B	psi-mi:“MI:0915”(physical association)	0.490
WLS	FAM241B	psi-mi:“MI:0915”(physical association)	0.400
MTNR1A	FAM241B	psi-mi:“MI:0915”(physical association)	0.370
FAM241B	ADRA1A	psi-mi:“MI:0915”(physical association)	0.370
WLS	FAM241B	psi-mi:“MI:0915”(physical association)	0.370
ERBB2	FAM241B	psi-mi:“MI:0915”(physical association)	0.370
ERBB3	FAM241B	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (111): C10orf35 (Two-hybrid), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS), C10orf35 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8GLK3, A0A974CYQ5, D2HWM5, D5LXJ0, P49950, P54731, Q0P5H8, Q15011, Q1LZE1, Q28DF1, Q3ZBU9, Q5HZY0, Q5R4I3, Q5R5B0, Q5XHH7, Q66HH4, Q6GPB6, Q6NRL6, Q6NYI0, Q6PCD5, Q6PCP5, Q6R755, Q7T321, Q7ZXQ3, Q803I8, Q80UY2, Q84L31, Q86TM6, Q8BGE4, Q8CIK8, Q8R317, Q8R3V6, Q8VCH8, Q924K2, Q92537, Q92575, Q96D05, Q9BSE4, Q9D882, Q9DBY1

Diamond homologs: Q8N8J7, Q96D05, Q9D882, Q9CZL2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 124 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
Signaling by ERBB2	5	21.4×	2e-04
Class A/1 (Rhodopsin-like receptors)	16	14.7×	3e-12
GPCR ligand binding	14	11.1×	4e-09
Signaling by GPCR	16	7.9×	2e-08
Transmission across Chemical Synapses	8	7.5×	5e-04
GPCR downstream signalling	14	7.5×	4e-07
Neurotransmitter receptors and postsynaptic signal transmission	6	7.4×	4e-03
Peptide ligand-binding receptors	7	6.4×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	8	15.2×	2e-05
positive regulation of cytosolic calcium ion concentration	11	11.2×	2e-06
calcium-mediated signaling	7	11.2×	4e-04
phospholipase C-activating G protein-coupled receptor signaling pathway	9	10.3×	4e-05
adenylate cyclase-activating G protein-coupled receptor signaling pathway	9	8.8×	1e-04
positive regulation of ERK1 and ERK2 cascade	11	8.1×	3e-05
G protein-coupled receptor signaling pathway	21	6.6×	5e-09
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	9	6.1×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

512 predictions. Top by Δscore:

Variant	Effect	Δscore
10:69630311:CAGG:C	donor_loss	1.0000
10:69630313:GGTG:G	donor_loss	1.0000
10:69630314:GTGA:G	donor_loss	1.0000
10:69630315:T:A	donor_loss	1.0000
10:69631702:A:AG	acceptor_gain	1.0000
10:69632783:A:AG	acceptor_gain	1.0000
10:69632789:GA:G	acceptor_gain	1.0000
10:69630310:GCAG:G	donor_gain	0.9900
10:69630314:G:GG	donor_gain	0.9900
10:69631700:ACAAT:A	acceptor_gain	0.9900
10:69631701:C:G	acceptor_gain	0.9900
10:69631702:AAT:A	acceptor_gain	0.9900
10:69631705:GCA:G	acceptor_loss	0.9900
10:69631706:CA:C	acceptor_loss	0.9900
10:69631708:G:A	acceptor_loss	0.9900
10:69631835:GACAG:G	donor_gain	0.9900
10:69631840:G:GA	donor_loss	0.9900
10:69631840:G:GG	donor_gain	0.9900
10:69632782:C:G	acceptor_gain	0.9900
10:69632784:T:G	acceptor_gain	0.9900
10:69632788:A:AG	acceptor_gain	0.9900
10:69632789:G:GA	acceptor_gain	0.9900
10:69632789:GAGC:G	acceptor_gain	0.9900
10:69631470:T:A	acceptor_gain	0.9800
10:69631478:A:AG	acceptor_gain	0.9800
10:69631479:G:GG	acceptor_gain	0.9800
10:69632781:A:AG	acceptor_gain	0.9800
10:69632787:CAG:C	acceptor_gain	0.9800
10:69632787:CAGAG:C	acceptor_gain	0.9800
10:69632788:AGA:A	acceptor_gain	0.9800

AlphaMissense

779 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:69631754:T:C	I4T	0.998
10:69631766:G:T	G8V	0.998
10:69633021:G:C	G110R	0.998
10:69631765:G:T	G8W	0.997
10:69633022:G:A	G110D	0.997
10:69633006:G:C	G105R	0.995
10:69631754:T:G	I4S	0.994
10:69631772:T:G	I10S	0.994
10:69633010:T:A	L106H	0.993
10:69631772:T:A	I10N	0.992
10:69632920:T:C	F76S	0.992
10:69632928:T:A	W79R	0.992
10:69632928:T:C	W79R	0.992
10:69632997:G:C	G102R	0.992
10:69633019:T:A	V109D	0.992
10:69631754:T:A	I4N	0.991
10:69631766:G:A	G8E	0.991
10:69632974:T:G	L94R	0.991
10:69633013:T:A	L107H	0.991
10:69631772:T:C	I10T	0.990
10:69633010:T:G	L106R	0.990
10:69632905:T:C	L71P	0.989
10:69633007:G:A	G105D	0.989
10:69632977:T:G	L95R	0.988
10:69632983:T:G	L97R	0.988
10:69633013:T:G	L107R	0.988
10:69633028:T:A	V112D	0.988
10:69632971:T:G	L93R	0.987
10:69632974:T:A	L94H	0.987
10:69632998:G:T	G102V	0.987

dbSNP variants (sampled 300 via entrez): RS1000455268 (10:69633867 G>T), RS1002035953 (10:69632415 G>A), RS1002698837 (10:69629685 T>C), RS1002930281 (10:69633379 G>A), RS1003210981 (10:69632032 C>G), RS1003703926 (10:69630804 G>A), RS1004514859 (10:69633910 G>A), RS1005216375 (10:69631235 C>G), RS1006463565 (10:69629859 C>T), RS1006845292 (10:69630054 G>A), RS1007250951 (10:69629366 G>A), RS1008508884 (10:69628568 T>A), RS1009260038 (10:69632390 G>A), RS1010301183 (10:69633683 C>T), RS1010649632 (10:69632104 T>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

5 associations (top):

Study	Trait	p-value
GCST002352_4	Type 2 diabetes	5.000000e-06
GCST003487_4	Response to fenofibrate (total cholesterol levels)	2.000000e-06
GCST006867_108	Type 2 diabetes	7.000000e-09
GCST007356_1	Antidepressant treatment resistance (number of drugs prescribed)	2.000000e-07
GCST007702_8	Triglyceride levels	1.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007806	total cholesterol change measurement
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, affects methylation	5
Valproic Acid	increases expression, affects expression, increases methylation, affects cotreatment	3
Cadmium Chloride	increases abundance, increases expression	3
Aflatoxin B1	decreases methylation, increases methylation	2
aristolochic acid I	increases expression	1
daidzein	affects cotreatment, affects expression	1
methylmercuric chloride	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
daidzin	affects cotreatment, affects expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
cupric oxide	increases expression	1
genistin	affects cotreatment, affects expression	1
glycitein	affects cotreatment, affects expression	1
glycitin	affects cotreatment, affects expression	1
ICG 001	increases expression	1
jinfukang	increases expression	1
(+)-JQ1 compound	decreases expression	1
NSC668394	increases expression	1
Bortezomib	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Cadmium	increases abundance, increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Ivermectin	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tunicamycin	decreases expression	1

Clinical trials (associated diseases)

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