FAM246A

Summary

FAM246A (family with sequence similarity 246 member A, HGNC:54844) is a protein-coding gene on chromosome 22q11.21, encoding Protein FAM246A (A0A494C0Y3).

At a glance

• MANE Select transcript: NM_001396025

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:54844
Approved symbol	FAM246A
Name	family with sequence similarity 246 member A
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000286102
Ensembl biotype	protein_coding
Entrez	117134598

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000652479

RefSeq mRNA: 1 — MANE Select: NM_001396025 NM_001396025

CCDS: CCDS93124

Canonical transcript exons

ENST00000652479 — 1 exons

Exon	Start	End
ENSE00003850016	21360601	21361299

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 37.20.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	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
hindlimb stylopod muscle	UBERON:0004252	35.32	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
superior frontal gyrus	UBERON:0002661	32.80	gold quality
prefrontal cortex	UBERON:0000451	31.91	silver quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
liver	UBERON:0002107	29.95	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
frontal cortex	UBERON:0001870	29.82	silver quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
cerebral cortex	UBERON:0000956	27.53	silver quality
leukocyte	CL:0000738	27.16	gold quality
monocyte	CL:0000576	27.11	gold quality
tonsil	UBERON:0002372	27.05	gold quality
blood	UBERON:0000178	27.02	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
anterior cingulate cortex	UBERON:0009835	25.91	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
urinary bladder	UBERON:0001255	25.72	gold quality
right testis	UBERON:0004534	25.61	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.46

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam246a	ENSMUSG00000116652
rattus_norvegicus	LOC120095536	ENSRNOG00000070676

Paralogs (2): FAM246C (ENSG00000286025), FAM246B (ENSG00000286175)

Protein

Protein identifiers

Protein FAM246A — A0A494C0Y3 (reviewed: A0A494C0Y3)

All UniProt accessions (1): A0A494C0Y3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM246 family.

RefSeq proteins (1): NP_001382954* (*=MANE)

Domains & families (InterPro)

UniProt features (6 total): region of interest 3, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A494C0Y3-F1	65.82	0.19

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_2H_DN, chr22q11

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:

ESM2 similar proteins: A0A140LIT1, A0A1B0GVG4, A0A494C0Y3, A0JNH6, A0JNN8, A1A5D9, A2ARS0, A5A769, A5PJP1, A6NC98, A7YWC8, C9JTQ0, O15049, O35764, O95502, P0C7N4, P0DPE3, P58660, Q0P5D1, Q1HCM0, Q2TAC2, Q3LUD3, Q3LUD4, Q3TMW1, Q3UMT1, Q4QRL3, Q5BLP8, Q5JTB6, Q6QNY0, Q6QZQ4, Q8BP01, Q8C7U1, Q8CHW5, Q8K262, Q8N283, Q8N6Y0, Q8TAT2, Q8TER5, Q8TF21, Q91XV7

Diamond homologs: A0A494C0N9, A0A494C0Y3, P0DSO1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1422 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:21360646:C:A	K218N	0.901
22:21360646:C:G	K218N	0.901
22:21360875:A:G	L142P	0.893
22:21361012:G:C	C96W	0.859
22:21361014:A:G	C96R	0.856
22:21360941:A:G	L120P	0.844
22:21360866:T:A	E145V	0.843
22:21361013:C:G	C96S	0.835
22:21361014:A:T	C96S	0.835
22:21361004:C:T	C99Y	0.828
22:21361004:C:G	C99S	0.824
22:21361005:A:T	C99S	0.824
22:21361013:C:T	C96Y	0.823
22:21360887:A:G	L138P	0.809
22:21360885:G:T	R139S	0.801
22:21361001:C:A	G100V	0.801
22:21361002:C:A	G100W	0.796
22:21361003:G:C	C99W	0.793
22:21360918:G:T	R128S	0.788
22:21360917:C:G	R128P	0.784
22:21360875:A:T	L142H	0.779
22:21360863:A:G	L146P	0.778
22:21361005:A:G	C99R	0.763
22:21361133:A:T	L56H	0.762
22:21360647:T:A	K218M	0.761
22:21360854:A:G	L149P	0.761
22:21360896:A:C	I135S	0.760
22:21360924:C:G	A126P	0.757
22:21360884:C:G	R139P	0.752
22:21360949:C:A	E117D	0.752

dbSNP variants (sampled 300 via entrez): RS1001463393 (22:21361316 A>C,G), RS1001539991 (22:21359607 T>G), RS1001767428 (22:21361522 G>T), RS1003033063 (22:21363197 A>G), RS1003127913 (22:21362644 C>G), RS1004382322 (22:21359328 T>C), RS1005074126 (22:21359156 G>A), RS1005651956 (22:21360928 G>C,T), RS1005943236 (22:21362080 C>A), RS1006388547 (22:21362252 G>A), RS1009793944 (22:21360764 A>G), RS1009933033 (22:21361631 G>A), RS1010013535 (22:21360052 G>A), RS1010314793 (22:21361334 G>A,C), RS1011573835 (22:21362695 G>A,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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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