FAM240C

Summary

FAM240C (family with sequence similarity 240 member C, HGNC:54200) is a protein-coding gene on chromosome 2q37.3, encoding Protein FAM240C (A0A1B0GVR7).

At a glance

• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001382368

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:54200
Approved symbol	FAM240C
Name	family with sequence similarity 240 member C
Location	2q37.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000216921
Ensembl biotype	protein_coding
Entrez	285095

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000401641, ENST00000404031, ENST00000452112

RefSeq mRNA: 3 — MANE Select: NM_001382368 NM_001382368, NM_001382369, NM_001382370

CCDS: CCDS92995, CCDS92996

Canonical transcript exons

ENST00000404031 — 3 exons

Exon	Start	End
ENSE00001556675	241893988	241894339
ENSE00001559012	241900358	241900464
ENSE00003799070	241897186	241897334

Expression profiles

Bgee: expression breadth ubiquitous, 126 present calls, max score 89.97.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1621 / max 77.2422, expressed in 22 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
34956	0.0822	16
34955	0.0470	12
34957	0.0329	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	89.97	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.18	gold quality
putamen	UBERON:0001874	79.61	gold quality
amygdala	UBERON:0001876	79.05	gold quality
temporal lobe	UBERON:0001871	78.72	gold quality
hindlimb stylopod muscle	UBERON:0004252	78.48	gold quality
substantia nigra	UBERON:0002038	77.75	gold quality
caudate nucleus	UBERON:0001873	77.58	gold quality
pancreas	UBERON:0001264	77.38	gold quality
nucleus accumbens	UBERON:0001882	76.50	gold quality
hypothalamus	UBERON:0001898	74.56	gold quality
anterior cingulate cortex	UBERON:0009835	74.55	gold quality
gastrocnemius	UBERON:0001388	73.34	gold quality
right frontal lobe	UBERON:0002810	73.34	gold quality
right lobe of thyroid gland	UBERON:0001119	73.27	gold quality
left lobe of thyroid gland	UBERON:0001120	72.84	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	72.65	gold quality
thyroid gland	UBERON:0002046	72.35	gold quality
Ammon’s horn	UBERON:0001954	72.19	gold quality
muscle of leg	UBERON:0001383	70.90	gold quality
prostate gland	UBERON:0002367	70.39	gold quality
Brodmann (1909) area 9	UBERON:0013540	70.22	gold quality
right hemisphere of cerebellum	UBERON:0014890	69.28	gold quality
cerebellum	UBERON:0002037	69.04	gold quality
cerebellar cortex	UBERON:0002129	68.93	gold quality
cerebellar hemisphere	UBERON:0002245	68.87	gold quality
primary visual cortex	UBERON:0002436	67.85	gold quality
brain	UBERON:0000955	67.74	gold quality
left uterine tube	UBERON:0001303	66.80	gold quality
superior frontal gyrus	UBERON:0002661	66.29	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.65

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Protein FAM240C — A0A1B0GVR7 (reviewed: A0A1B0GVR7)

All UniProt accessions (2): A0A1B0GVR7, A0A1B0GUP9

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM240 family.

RefSeq proteins (3): NP_001369297, NP_001369298, NP_001369299 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040261	FAM240	Family

UniProt features (3 total): chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GVR7-F1	79.68	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): SIX1_TARGET_GENES, chr2q37, KONIGORSKI_INCREASED_SUBCUTANEOUS_ADIPOSE_TISSUE_MASS_DN, GSE25088_CTRL_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DN, GSE23114_PERITONEAL_CAVITY_B1A_BCELL_VS_SPLEEN_BCELL_IN_SLE2C1_MOUSE_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

156 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAM240C	TMDD1	P0DPE3	795
FAM240C	SCYGR7	A0A286YF01	794
FAM240C	SMIM38	A0A286YFK9	794
FAM240C	SMIM28	A0A1B0GU29	763
FAM240C	ETDA	Q3ZM63	717
FAM240C	ETDC	A0A1B0GVM5	716
FAM240C	SCYGR1	A0A286YEY9	670
FAM240C	SMIM36	A0A1B0GVT2	625
FAM240C	SMIM41	A0A2R8YCJ5	623
FAM240C	C1orf232	A0A0U1RR37	621
FAM240C	EDDM13	A0A1B0GTR0	621
FAM240C	CCDC201	A0A1B0GTI1	571
FAM240C	C10orf143	A0A1B0GUT2	530
FAM240C	SPAAR	A0A1B0GVQ0	529
FAM240C	MYMX	A0A1B0GTQ4	480

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GVR7, A0PJW8, A2BYT2, A5FRX9, B8G1X0, C1DKL7, G3UWD5, O42659, O62953, O95567, O98453, P05899, P11690, P11794, P19718, P20920, P27975, P32544, P33482, P39971, P52776, P54446, P69516, P69517, P86209, Q02781, Q0ABH1, Q1X6Y0, Q3AMN4, Q3J8R8, Q3K5Z2, Q3MFB7, Q3ZZM0, Q537H7, Q57P89, Q5I162, Q5PHY6, Q6AY31, Q75003, Q7CQJ0

Diamond homologs: A0A1B0GVK7, A0A1B0GVR7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	1
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

628 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:241897260:C:A	W29C	0.995
2:241897260:C:G	W29C	0.995
2:241897262:A:G	W29R	0.994
2:241897262:A:T	W29R	0.994
2:241894324:C:A	W59C	0.992
2:241894324:C:G	W59C	0.992
2:241897261:C:G	W29S	0.988
2:241897269:C:A	K26N	0.987
2:241897269:C:G	K26N	0.987
2:241897197:G:C	S50R	0.985
2:241897197:G:T	S50R	0.985
2:241897199:T:G	S50R	0.985
2:241897209:C:A	R46S	0.985
2:241897209:C:G	R46S	0.985
2:241894326:A:G	W59R	0.981
2:241894326:A:T	W59R	0.981
2:241894335:G:T	R56S	0.978
2:241897219:T:A	E43V	0.976
2:241897262:A:C	W29G	0.974
2:241897264:A:G	F28S	0.974
2:241897258:T:A	E30V	0.973
2:241897210:C:A	R46M	0.972
2:241894325:C:G	W59S	0.969
2:241897210:C:G	R46T	0.967
2:241897257:C:A	E30D	0.967
2:241897257:C:G	E30D	0.967
2:241897263:A:C	F28L	0.966
2:241897263:A:T	F28L	0.966
2:241897265:A:G	F28L	0.966
2:241894337:A:G	L55P	0.965

dbSNP variants (sampled 300 via entrez): RS1000021098 (2:241899129 G>C), RS1000205780 (2:241900941 A>G), RS1000262390 (2:241897388 C>A,T), RS1000482985 (2:241902832 G>T), RS1001177861 (2:241901835 A>G), RS1001256909 (2:241898541 G>A), RS1001342304 (2:241893685 G>T), RS1001352275 (2:241896323 C>T), RS1001852684 (2:241893934 T>A), RS1002195496 (2:241899223 C>T), RS1002199146 (2:241903255 G>A,C), RS1002792974 (2:241904265 C>T), RS1003177433 (2:241904365 GACTA>G), RS1003195077 (2:241900221 G>A,C), RS1003345070 (2:241895757 G>A)

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)

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs78233573	FAM240C		0.00	0

Clinical trials (associated diseases)

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