LRIF1

protein-coding

ligand dependent nuclear receptor interacting factor 1

Gene summary

Predicted to enable nuclear retinoic acid receptor binding activity. Involved in dosage compensation by inactivation of X chromosome. Located in Barr body; chromosome, telomeric region; and nucleoplasm. Implicated in facioscapulohumeral muscular dystrophy 3. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C1orf103

MANE transcript

NM_018372.4

Inheritance

ClinVar variants

P:2U:101B:7

Top phenotype

Facioscapulohumeral muscular dystrophy 3, digenic

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr1:110,947,190-110,963,965

External References & Databases

Ensembl (ENSG00000121931)

Transcript & Mutation Effects

hg38 • Region Span ~16.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

facioscapulohumeral muscular dystrophyMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0001347

Submitter: PanelApp Australia

facioscapulohumeral muscular dystrophy 3, digenicLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0030354

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LRIF1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 102

not providedTotal: 3

Facioscapulohumeral muscular dystrophy 3, digenicTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018372.4. 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	1 clinvar		2
missense			100 clinvar	6 clinvar		106
nonsense	1 clinvar					1
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	2	0	101	7	0	110

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018372.4	RefSeq	NP_060842.3	4	MANE Select
ENST00000369763.5	Ensembl	ENSP00000358778.4	4	MANE Select
NM_001006945.2	RefSeq	NP_001006946.1	2	Standard
ENST00000485275.2	Ensembl	ENSP00000432290.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
dosage compensation by inactivation of X chromosome

Molecular Function

protein binding
retinoic acid receptor binding

Cellular Component

nuclear chromosome, telomeric region
Barr body
nucleus
microtubule organizing center
nuclear matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369763
Coding exons: 4
Length: 16895
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125746
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.241	377	390	0.966	0.0000186	5043
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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