LIAT1

ligand of ATE1

Basic information

Region (hg38): 17:410325-431062

Previous symbols: [ "C17orf97" ]

Links

ENSG00000187624 ∙ NCBI:400566 ∙ ∙ HGNC:33800 ∙ Uniprot:Q6ZQX7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LIAT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIAT1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				12		12
missense			3	4		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	16	0

Variants in LIAT1

This is a list of pathogenic ClinVar variants found in the LIAT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-410406-C-G		not specified	Uncertain significance (Oct 29, 2021)
17-413224-G-C		not specified	Likely benign (Aug 02, 2021)
17-413224-G-T		not specified	Likely benign (Oct 12, 2021)
17-413464-C-T			Likely benign (Jul 01, 2023)
17-413485-C-T			Likely benign (Jun 01, 2023)
17-413494-C-T			Likely benign (Jun 01, 2023)
17-413500-C-T			Likely benign (Sep 01, 2024)
17-413506-C-T			Likely benign (Apr 01, 2024)
17-413515-C-T			Likely benign (May 01, 2024)
17-413531-G-A		not specified	Likely benign (Jun 11, 2021)
17-413545-C-T			Likely benign (Nov 01, 2023)
17-413552-C-A		not specified	Uncertain significance (Dec 27, 2023)
17-413591-G-A			Likely benign (Dec 01, 2023)
17-413614-C-T			Likely benign (Sep 01, 2024)
17-413635-C-T			Likely benign (Apr 01, 2025)
17-413644-C-T			Likely benign (Feb 01, 2023)
17-413734-C-T			Likely benign (Aug 01, 2024)
17-413755-C-T			Likely benign (Nov 01, 2023)
17-413845-C-T			Likely benign (Feb 01, 2023)
17-414083-C-T		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIAT1	protein_coding	protein_coding	ENST00000360127	2	13393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000484	0.0721	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0154	252	251	1.00	0.0000149	2721
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 1700016K19Rik
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)