LRATD2

LRAT domain containing 2, the group of LRAT domain containing family

Basic information

Region (hg38): 8:126552443-126558478

Previous symbols: [ "FAM84B" ]

Links

ENSG00000168672 ∙ NCBI:157638 ∙ OMIM:609483 ∙ HGNC:24166 ∙ Uniprot:Q96KN1 ∙ 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 LRATD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRATD2 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in LRATD2

This is a list of pathogenic ClinVar variants found in the LRATD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-126556498-G-A		not specified	Uncertain significance (Mar 06, 2023)
8-126556521-G-A		not specified	Uncertain significance (Jan 04, 2024)
8-126556557-G-A		not specified	Uncertain significance (Jun 24, 2022)
8-126556612-T-A		not specified	Uncertain significance (Dec 21, 2022)
8-126556786-C-G		not specified	Uncertain significance (Mar 15, 2024)
8-126556849-C-T		not specified	Uncertain significance (Jan 17, 2023)
8-126556882-G-C		not specified	Uncertain significance (Aug 02, 2023)
8-126556903-G-T		not specified	Uncertain significance (Jun 28, 2022)
8-126556974-T-C		not specified	Uncertain significance (Dec 19, 2022)
8-126556997-C-CGG			not provided (-)
8-126557048-G-C		not specified	Uncertain significance (Aug 26, 2022)
8-126557053-G-A		not specified	Uncertain significance (May 27, 2022)
8-126557149-C-A		not specified	Uncertain significance (Jan 24, 2023)
8-126557173-G-A		not specified	Uncertain significance (Mar 28, 2024)
8-126557209-C-T		not specified	Uncertain significance (Jun 17, 2024)
8-126557212-G-A		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRATD2	protein_coding	protein_coding	ENST00000304916	1	5952

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000366	0.632	124260	0	15	124275	0.0000604

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.596	165	188	0.878	0.00000863	1972
Missense in Polyphen		50	69.835	0.71598		721
Synonymous	-0.192	92	89.7	1.03	0.00000428	649
Loss of Function	0.678	6	8.08	0.743	3.46e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.000177	0.000164
Finnish	0.000188	0.000185
European (Non-Finnish)	0.0000576	0.0000537
Middle Eastern	0.000177	0.000164
South Asian	0.0000343	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.193
• hipred: Y
• hipred_score: 0.672
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam84b

Gene ontology

• Cellular component: cytoplasm;plasma membrane
• Molecular function: protein binding