GPM6B

glycoprotein M6B

Basic information

Region (hg38): X:13770938-13938638

Links

ENSG00000046653 ∙ NCBI:2824 ∙ OMIM:300051 ∙ HGNC:4461 ∙ Uniprot:Q13491 ∙ 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 GPM6B gene.

• Inborn genetic diseases (6 variants)
• not provided (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPM6B 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	2
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	5	2	1

Variants in GPM6B

This is a list of pathogenic ClinVar variants found in the GPM6B region.

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

Position	Type	Phenotype	Significance	ClinVar
X-13776244-A-G			Benign (May 08, 2018)
X-13776249-C-T		not specified	Uncertain significance (Mar 14, 2024)
X-13776267-C-T		not specified	Uncertain significance (Jan 26, 2022)
X-13777346-G-A		not specified	Likely benign (Dec 13, 2017)
X-13777400-G-A			Likely benign (Aug 01, 2022)
X-13779840-G-C		not specified	Uncertain significance (May 31, 2023)
X-13779874-G-A		not specified	Uncertain significance (May 23, 2023)
X-13783381-C-T		not specified	Uncertain significance (Dec 18, 2023)
X-13783432-G-A		not specified	Uncertain significance (Apr 25, 2023)
X-13785650-C-T		not specified	Likely benign (Nov 12, 2021)
X-13816882-G-T		not specified	Uncertain significance (May 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPM6B	protein_coding	protein_coding	ENST00000316715	8	167608

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.346	0.651	125475	4	1	125480	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	68	132	0.514	0.0000104	2155
Missense in Polyphen		13	29.236	0.44465		519
Synonymous	-0.413	59	55.1	1.07	0.00000508	621
Loss of Function	2.58	3	13.1	0.229	9.62e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000725	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000377	0.0000264
Middle Eastern	0.0000725	0.0000544
South Asian	0.0000714	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in neural development. Involved in regulation of osteoblast function and bone formation. Involved in matrix vesicle release by osteoblasts; this function seems to involve maintenance of the actin cytoskeleton. May be involved in cellular trafficking of SERT and thereby in regulation of serotonin uptake. {ECO:0000269|PubMed:21638316}.

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.175
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.927
• hipred: Y
• hipred_score: 0.761
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpm6b
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: ossification;nervous system development;protein transport;cell differentiation;positive regulation of bone mineralization;neuron projection development;regulation of actin cytoskeleton organization;negative regulation of serotonin uptake;regulation of focal adhesion assembly;extracellular matrix assembly;negative regulation of protein localization to cell surface
• Cellular component: plasma membrane;integral component of membrane;membrane raft
• Molecular function: molecular_function