LIAT1

protein-coding

ligand of ATE1

Gene summary

Predicted to enable molecular condensate scaffold activity. Predicted to be involved in membraneless organelle assembly and protein arginylation. Predicted to be located in cytoplasm. Predicted to be active in nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C17orf97

MANE transcript

NM_001013672.5

Inheritance

—

ClinVar variants

U:11B:23

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 2.59

Max pathogenic AF

—

Genomic locus

chr17:410,325-431,062

External References & Databases

Ensembl (ENSG00000187624)

Transcript & Mutation Effects

hg38 • Region Span ~20.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LIAT1 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 20

not specifiedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001013672.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	19 clinvar		20
missense			9 clinvar	4 clinvar		13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	11	23	0	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001013672.5	RefSeq	NP_001013694.4	2	MANE Select
ENST00000360127.7	Ensembl	ENSP00000353245.6	2	MANE Select
ENST00000491373.1	Ensembl	ENSP00000419482.1	3	Standard
ENST00000571106.1	Ensembl	ENSP00000458320.1	2	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360127
Coding exons: 2
Length: 13393
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0154	252	251	1.00	0.0000149	2721
Missense (PolyPhen)		92	99.749	0.92231		1086
Synonymous	-0.273	122	118	1.03	0.00000840	846
Loss of Function	-2.25	6	2.31	2.59	1.01e-7	31

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in ATE1-mediated N-terminal arginylation. {ECO:0000250|UniProtKB:Q810M6}.;

Intolerance Scores

LoFtool: 0.945
RVIS EVS: 1.15
RVIS percentile EVS: 92.52

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium