LRATD1

LRAT domain containing 1, the group of LRAT domain containing family

Basic information

Region (hg38): 2:14632700-14650814

Previous symbols: [ "FAM84A" ]

Links

ENSG00000162981 ∙ NCBI:151354 ∙ OMIM:611234 ∙ HGNC:20743 ∙ Uniprot:Q96KN4 ∙ 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 LRATD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRATD1 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						0
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in LRATD1

This is a list of pathogenic ClinVar variants found in the LRATD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-14634060-C-G		not specified	Uncertain significance (Jan 04, 2024)
2-14634080-C-G		not specified	Uncertain significance (Sep 12, 2023)
2-14634099-T-G		not specified	Likely benign (Feb 06, 2024)
2-14634155-C-T		not specified	Uncertain significance (Sep 20, 2023)
2-14634389-C-T		not specified	Uncertain significance (Jan 10, 2022)
2-14634484-G-A		not specified	Uncertain significance (Feb 22, 2024)
2-14634494-C-G		not specified	Uncertain significance (Mar 17, 2023)
2-14634592-G-C		not specified	Uncertain significance (Jun 01, 2023)
2-14634723-C-G		not specified	Uncertain significance (Jul 27, 2021)
2-14634788-G-A		not specified	Uncertain significance (Jan 05, 2022)
2-14634809-G-A		not specified	Uncertain significance (Apr 01, 2024)
2-14634847-G-T		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRATD1	protein_coding	protein_coding	ENST00000295092	1	18124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.888	0.111	125414	0	2	125416	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.496	137	154	0.888	0.00000693	1862
Missense in Polyphen		45	63.333	0.71053		743
Synonymous	-1.12	82	70.1	1.17	0.00000335	591
Loss of Function	2.47	0	7.12	0.00	3.06e-7	84

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)	0.0000180	0.00000882
Middle Eastern	0.00	0.00
South Asian	0.0000377	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0813

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.429
• ghis: 0.655

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.274

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam84a