LITAFD

Summary

LITAFD (LITAF domain containing, HGNC:53927) is a protein-coding gene on chromosome 16p13.2, encoding LITAF domain-containing protein (A0A1B0GVX0).

Predicted to enable zinc ion binding activity. Predicted to be involved in regulation of cytokine production. Predicted to be located in membrane. Predicted to be active in cytoplasmic side of late endosome membrane; cytoplasmic side of lysosomal membrane; and nucleus.

Source: NCBI Gene 101929989 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001395433

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53927
Approved symbol	LITAFD
Name	LITAF domain containing
Location	16p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283516
Ensembl biotype	protein_coding
Entrez	101929989

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000636296, ENST00000637237, ENST00000637929, ENST00000850638, ENST00000850639

RefSeq mRNA: 2 — MANE Select: NM_001395433 NM_001395433, NM_001395434

CCDS: CCDS92105

Canonical transcript exons

ENST00000636296 — 4 exons

Exon	Start	End
ENSE00003794227	8884323	8884465
ENSE00003800342	8883210	8883286
ENSE00003978210	8882351	8882510
ENSE00004282421	8885187	8885350

Expression profiles

Bgee: expression breadth broad, 49 present calls, max score 75.67.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0113 / max 10.8260, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152671	0.0113	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.67	gold quality
left testis	UBERON:0004533	72.36	gold quality
right testis	UBERON:0004534	72.09	gold quality
testis	UBERON:0000473	71.60	gold quality
sural nerve	UBERON:0015488	51.09	gold quality
adenohypophysis	UBERON:0002196	46.11	gold quality
lower esophagus mucosa	UBERON:0035834	46.09	silver quality
bone marrow	UBERON:0002371	45.92	gold quality
pituitary gland	UBERON:0000007	44.74	gold quality
bone marrow cell	CL:0002092	43.73	gold quality
granulocyte	CL:0000094	43.60	silver quality
right lobe of liver	UBERON:0001114	42.11	gold quality
right hemisphere of cerebellum	UBERON:0014890	42.10	silver quality
metanephros cortex	UBERON:0010533	40.25	gold quality
right adrenal gland cortex	UBERON:0035827	40.18	silver quality
liver	UBERON:0002107	39.33	silver quality
right ovary	UBERON:0002118	38.54	silver quality
right coronary artery	UBERON:0001625	38.32	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
cortex of kidney	UBERON:0001225	37.05	silver quality
tonsil	UBERON:0002372	36.85	gold quality
apex of heart	UBERON:0002098	36.76	gold quality
skeletal muscle tissue	UBERON:0001134	36.73	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
right adrenal gland	UBERON:0001233	35.24	silver quality
primary visual cortex	UBERON:0002436	35.17	silver quality
blood	UBERON:0000178	35.10	silver quality
muscle tissue	UBERON:0002385	33.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.94

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Litafd	ENSMUSG00000107252
rattus_norvegicus	Litafd	ENSRNOG00000055413

Protein

Protein identifiers

LITAF domain-containing protein — A0A1B0GVX0 (reviewed: A0A1B0GVX0)

Alternative names: LITAF-like protein

All UniProt accessions (2): A0A1B0GVX0, A0A1B0GTQ0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Domain organisation. The LITAF domain is stabilized by a bound zinc ion. The LITAF domain contains an amphipathic helix that mediates interaction with lipid membranes.

Similarity. Belongs to the CDIP1/LITAF family.

RefSeq proteins (2): NP_001382362, NP_001382363 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006629	LITAF	Domain
IPR037519	LITAF_fam	Family

Pfam: PF10601

UniProt features (7 total): binding site 4, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GVX0-F1	63.60	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.

Ligand- & substrate-binding residues (4): 7; 10; 59; 62

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 13 (showing top): GOCC_VACUOLAR_MEMBRANE, GOBP_CYTOKINE_PRODUCTION, GOCC_LATE_ENDOSOME_MEMBRANE, GOCC_CYTOPLASMIC_SIDE_OF_MEMBRANE, GOCC_SIDE_OF_MEMBRANE, GOCC_CYTOPLASMIC_SIDE_OF_LYSOSOMAL_MEMBRANE, GOCC_ENDOSOME_MEMBRANE, GOCC_LATE_ENDOSOME, GOCC_CYTOPLASMIC_SIDE_OF_ENDOSOME_MEMBRANE, GOCC_VACUOLE, GOCC_ENDOSOME, GOCC_VESICLE_MEMBRANE, chr16p13

GO Biological Process (1): regulation of cytokine production (GO:0001817)

GO Molecular Function (2): zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasmic side of late endosome membrane (GO:0098560), cytoplasmic side of lysosomal membrane (GO:0098574), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytokine production	1
regulation of gene expression	1
regulation of multicellular organismal process	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1
cytoplasmic side of endosome membrane	1
late endosome membrane	1
lysosomal membrane	1
cytoplasmic side of membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

336 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LITAFD	OR6N1	Q8NGY5	659
LITAFD	OR6N2	Q8NGY6	641
LITAFD	OR2C1	O95371	623
LITAFD	H3BQ15	H3BQ15	553
LITAFD	AMDHD2	Q9Y303	550
LITAFD	RCBTB1	Q8NDN9	518
LITAFD	CARHSP1	Q9Y2V2	494
LITAFD	NUBPL	Q8TB37	455
LITAFD	PHF11	Q9UIL8	416
LITAFD	PTP4A1	Q93096	404
LITAFD	SETDB2	Q96T68	391
LITAFD	FIG4	Q92562	349
LITAFD	IL6	P05231	348
LITAFD	IL1B	P01584	347
LITAFD	HNF4G	Q14541	345

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GVX0, A2ADU8, A2ADU9, A2Y075, A6QP72, O82232, P34655, P55017, P55018, P56508, P59158, P68178, P68179, Q0DKW8, Q0VBW2, Q22701, Q3ZCB2, Q53GD3, Q54RZ2, Q5REK4, Q5RJI2, Q5TYP8, Q66I68, Q6DK93, Q6DK99, Q6E1M8, Q6E213, Q6GMG8, Q6GZQ0, Q6NUC1, Q6P828, Q6PCW6, Q6ZPD8, Q8H5T6, Q8NG11, Q8QZY6, Q8S5M8, Q91VA1, Q9ARD5, Q9BYD5

Diamond homologs: A0A1B0GVX0, P0C0T0, Q54HX8, Q6GMG8, Q6GZQ0, Q6P828, Q8QGW7, Q99732, Q9JLJ0, Q58D45, Q5BJ83, Q5U2U6, Q8AVW3, Q9DB75, Q9H305

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

2 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	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

459 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:8885215:T:C	F47L	0.746
16:8885217:C:A	F47L	0.746
16:8885217:C:G	F47L	0.746
16:8885275:T:C	F67L	0.697
16:8885277:C:A	F67L	0.697
16:8885277:C:G	F67L	0.697

dbSNP variants (sampled 300 via entrez): RS1000334851 (16:8885322 G>A,C), RS1000430711 (16:8880970 T>C), RS1000577178 (16:8881268 G>A), RS1001018315 (16:8883504 C>G), RS1001343870 (16:8884331 C>T), RS1002963295 (16:8881556 C>A,T), RS1003236815 (16:8884812 C>T), RS1003297017 (16:8882642 C>A), RS1003349365 (16:8882473 A>G), RS1003615444 (16:8884565 C>A,G), RS1003751088 (16:8880540 G>A), RS1003955180 (16:8883561 A>C,G), RS1004216008 (16:8884070 TAAA>T), RS1004804233 (16:8883756 G>A,T), RS1005042135 (16:8883001 A>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

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.