LRIF1

ligand dependent nuclear receptor interacting factor 1

Basic information

Region (hg38): 1:110947189-110963965

Previous symbols: [ "C1orf103" ]

Links

ENSG00000121931 ∙ NCBI:55791 ∙ OMIM:615354 ∙ HGNC:30299 ∙ Uniprot:Q5T3J3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• facioscapulohumeral muscular dystrophy 3, digenic (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRIF1 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRIF1 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				1		1
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in LRIF1

This is a list of pathogenic ClinVar variants found in the LRIF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-110947994-G-T		not specified	Uncertain significance (May 04, 2022)
1-110948007-C-G		not specified	Uncertain significance (Feb 10, 2023)
1-110948023-T-C		not specified	Uncertain significance (Nov 15, 2021)
1-110948068-G-A		not specified	Uncertain significance (Sep 28, 2021)
1-110948093-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-110948095-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-110948255-T-C		not specified	Uncertain significance (May 18, 2023)
1-110948293-T-A		not specified	Uncertain significance (Feb 07, 2023)
1-110948312-T-C		not specified	Uncertain significance (Dec 14, 2023)
1-110948350-T-C		not specified	Uncertain significance (Sep 07, 2022)
1-110950119-T-C		not specified	Uncertain significance (Mar 14, 2023)
1-110951337-G-C		not specified	Uncertain significance (Feb 13, 2024)
1-110951337-G-T		not specified	Uncertain significance (Apr 22, 2022)
1-110951401-C-T		not specified	Uncertain significance (Oct 05, 2023)
1-110951455-T-C		not specified	Likely benign (Jul 26, 2022)
1-110951470-A-C		not specified	Uncertain significance (Dec 12, 2023)
1-110951520-G-T		not specified	Uncertain significance (Aug 13, 2021)
1-110951524-T-C		not specified	Uncertain significance (Dec 14, 2022)
1-110951662-A-C		not specified	Uncertain significance (Aug 28, 2023)
1-110951665-T-G		not specified	Uncertain significance (Jan 31, 2022)
1-110951677-G-T		not specified	Uncertain significance (Feb 05, 2024)
1-110951755-A-G		not specified	Uncertain significance (Sep 28, 2022)
1-110951849-C-T			Likely benign (Sep 01, 2022)
1-110952011-C-CCATT		Facioscapulohumeral muscular dystrophy 3, digenic	Pathogenic (Aug 16, 2021)
1-110952100-T-C		not specified	Uncertain significance (Feb 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRIF1	protein_coding	protein_coding	ENST00000369763	4	16895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000434	0.998	125733	0	13	125746	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.241	377	390	0.966	0.0000186	5043
Missense in Polyphen		76	91.679	0.82898		1067
Synonymous	0.624	134	144	0.934	0.00000734	1531
Loss of Function	2.77	10	24.9	0.401	0.00000127	342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000659	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Together with SMCHD1, involved in chromosome X inactivation in females by promoting the compaction of heterochromatin (PubMed:23542155). Also able to repress the ligand-induced transcriptional activity of retinoic acid receptor alpha (RARA), possibly through direct recruitment of histone deacetylases (PubMed:17455211). {ECO:0000269|PubMed:17455211, ECO:0000269|PubMed:23542155}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.0652
• hipred: N
• hipred_score: 0.145
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrif1

Gene ontology

• Biological process: regulation of transcription, DNA-templated;dosage compensation by inactivation of X chromosome
• Cellular component: nuclear chromosome, telomeric region;Barr body;nucleus;microtubule organizing center;nuclear matrix
• Molecular function: protein binding;retinoic acid receptor binding