MILR1

mast cell immunoglobulin like receptor 1, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 17:64449037-64492770

Previous symbols: [ "C17orf60" ]

Links

ENSG00000271605 ∙ NCBI:284021 ∙ ∙ HGNC:27570 ∙ Uniprot:Q7Z6M3 ∙ 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 MILR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MILR1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

Variants in MILR1

This is a list of pathogenic ClinVar variants found in the MILR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-64477734-A-G			Likely benign (Jun 14, 2018)
17-64477825-A-G			Uncertain significance (Aug 10, 2023)
17-64477836-G-A			Uncertain significance (Jul 11, 2022)
17-64477837-C-A		Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4	Uncertain significance (Oct 05, 2022)
17-64477846-T-C			Uncertain significance (Nov 22, 2022)
17-64477850-C-T			Likely benign (Nov 24, 2023)
17-64477852-TAATC-T			Uncertain significance (Jan 16, 2024)
17-64477856-CAA-C		Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4	Pathogenic (Aug 01, 2011)
17-64477864-C-T		Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4 • Hereditary spastic paraplegia	Conflicting classifications of pathogenicity (Jan 27, 2024)
17-64477880-A-G			Likely benign (Nov 17, 2023)
17-64477895-C-T			Uncertain significance (Aug 17, 2022)
17-64477897-T-C			Uncertain significance (Aug 09, 2022)
17-64477900-T-C			Uncertain significance (Nov 07, 2023)
17-64477916-C-A			Likely benign (Jan 26, 2022)
17-64477918-G-T		Hereditary spastic paraplegia	Uncertain significance (Feb 14, 2023)
17-64477929-C-T		Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4 • POLG2-related disorder	Likely pathogenic (Aug 23, 2023)
17-64477930-C-G			Uncertain significance (May 02, 2023)
17-64477932-T-G			Uncertain significance (Sep 22, 2023)
17-64477933-TCTCCA-T		Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4	Uncertain significance (Oct 11, 2018)
17-64477935-T-G			Uncertain significance (Apr 06, 2022)
17-64477937-C-A			Uncertain significance (Jan 01, 2022)
17-64477941-G-C			Uncertain significance (Jul 26, 2022)
17-64477942-T-C			Uncertain significance (Apr 17, 2023)
17-64477952-A-G			Likely benign (Dec 24, 2023)
17-64477957-A-C			Uncertain significance (Oct 30, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MILR1	protein_coding	protein_coding	ENST00000605096	4	3192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0245	0.792	120418	13	590	121021	0.00249

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.540	36	46.3	0.777	0.00000233	569
Missense in Polyphen		12	12.952	0.92652		139
Synonymous	1.09	11	16.7	0.660	8.98e-7	161
Loss of Function	0.984	3	5.49	0.547	2.30e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000126
Ashkenazi Jewish	0.000628	0.000609
East Asian	0.000120	0.000114
Finnish	0.00	0.00
European (Non-Finnish)	0.0000389	0.0000365
Middle Eastern	0.000120	0.000114
South Asian	0.0215	0.0200
Other	0.00107	0.00102

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Immunoglobulin-like receptor which plays an inhibitory role in degranulation of mast cells. Negatively regulates IgE- mediated mast cell activation and suppresses the type I immediate hypersensitivity reaction (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0719

Haploinsufficiency Scores

• pHI: 0.0418

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Mouse Genome Informatics

• Gene name: Milr1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: negative regulation of mast cell activation;mast cell degranulation
• Cellular component: integral component of plasma membrane;mast cell granule