GLMP

protein-coding

glycosylated lysosomal membrane protein

Gene summary

Involved in positive regulation of transcription by RNA polymerase II. Located in cytosol; lysosome; and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C1orf85

MANE transcript

NM_144580.3

Inheritance

—

ClinVar variants

U:69B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr1:156,290,089-156,295,689

External References & Databases

Ensembl (ENSG00000198715)

Transcript & Mutation Effects

hg38 • Region Span ~5.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GLMP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144580.3. 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			2 clinvar			2
missense			65 clinvar	4 clinvar	1 clinvar	70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	69	4	1	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144580.3	RefSeq	NP_653181.1	6	MANE Select
ENST00000362007.6	Ensembl	ENSP00000354553.1	6	MANE Select
NM_001256604.2	RefSeq	NP_001243533.1	6	Standard
NM_001256605.2	RefSeq	NP_001243534.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity
transcription regulatory region DNA binding

Cellular Component

nucleus
lysosome
lysosomal membrane
cytosol
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000362007
Coding exons: 6
Length: 5584
Individuals with no LoFs: 125669
Homozygous LoFs: 0
Heterozygous LoFs: 79
Defined: 125748
p: 0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.848	185	220	0.839	0.0000119	2573
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00065	0.00065	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00025	0.00025	rare
South Asian	0.00098	0.00098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0941

Intolerance Scores

RVIS EVS: 0.02
RVIS percentile EVS: 55.61

Essentials

Essential (gene trap): N