GLMP

glycosylated lysosomal membrane protein

Basic information

Region (hg38): 1:156290089-156295689

Previous symbols: [ "C1orf85" ]

Links

ENSG00000198715 ∙ NCBI:112770 ∙ OMIM:619958 ∙ HGNC:29436 ∙ Uniprot:Q8WWB7 ∙ 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 GLMP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLMP 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			41	2	1	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	1

Variants in GLMP

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

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

Position	Type	Phenotype	Significance	ClinVar
1-156291390-T-C		not specified	Uncertain significance (Oct 03, 2024)
1-156291409-C-T			Likely benign (May 09, 2018)
1-156291419-T-A		not specified	Uncertain significance (May 14, 2024)
1-156291441-G-C		not specified	Uncertain significance (Aug 02, 2022)
1-156291458-C-G		not specified	Uncertain significance (Mar 29, 2023)
1-156291488-T-C		not specified	Uncertain significance (Jul 02, 2024)
1-156291491-A-G		not specified	Uncertain significance (Jun 18, 2021)
1-156291507-C-T		not specified	Uncertain significance (Dec 16, 2023)
1-156291537-G-C		not specified	Uncertain significance (Jan 27, 2025)
1-156291543-A-T		not specified	Uncertain significance (Jan 24, 2025)
1-156291548-C-T		not specified	Uncertain significance (Feb 06, 2024)
1-156291549-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-156291590-T-A		not specified	Uncertain significance (Feb 28, 2023)
1-156293088-G-C		not specified	Uncertain significance (Jul 05, 2024)
1-156293100-C-T		not specified	Uncertain significance (Sep 25, 2024)
1-156293105-C-T		not specified	Uncertain significance (Aug 02, 2023)
1-156293114-A-G		not specified	Uncertain significance (Aug 16, 2021)
1-156293154-G-C			Benign (May 04, 2018)
1-156293172-C-T		not specified	Uncertain significance (May 21, 2024)
1-156293207-G-A		not specified	Uncertain significance (Oct 19, 2024)
1-156293333-G-A		not specified	Uncertain significance (Apr 06, 2023)
1-156293333-G-C		not specified	Uncertain significance (Dec 05, 2024)
1-156293339-C-G		not specified	Uncertain significance (Jan 17, 2024)
1-156293371-G-A		not specified	Uncertain significance (Jan 29, 2024)
1-156293377-T-C		not specified	Uncertain significance (Mar 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLMP	protein_coding	protein_coding	ENST00000362007	6	5584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.42e-11	0.0543	125669	0	79	125748	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.848	185	220	0.839	0.0000119	2573
Missense in Polyphen		43	55.975	0.7682		674
Synonymous	0.940	88	100	0.880	0.00000589	906
Loss of Function	0.115	17	17.5	0.970	0.00000111	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000274
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000653	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000251	0.000246
Middle Eastern	0.000653	0.000653
South Asian	0.000980	0.000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0941

Intolerance Scores

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• pHI: 0.0736
• hipred: N
• hipred_score: 0.144
• ghis: 0.469

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Glmp
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; pigmentation phenotype; immune system phenotype

Gene ontology

• Biological process: positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;lysosome;lysosomal membrane;cytosol;integral component of membrane
• Molecular function: DNA-binding transcription factor activity;transcription regulatory region DNA binding