GINM1

glycosylated integral membrane protein 1

Basic information

Region (hg38): 6:149566293-149591748

Previous symbols: [ "C6orf72" ]

Links

ENSG00000055211 ∙ NCBI:116254 ∙ ∙ HGNC:21074 ∙ Uniprot:Q9NU53 ∙ 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 GINM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GINM1 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in GINM1

This is a list of pathogenic ClinVar variants found in the GINM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149566421-G-A		not specified	Uncertain significance (May 31, 2023)
6-149566524-G-A		not specified	Uncertain significance (Aug 04, 2023)
6-149572285-G-A		not specified	Uncertain significance (Jan 23, 2024)
6-149572330-A-G		not specified	Likely benign (Jul 05, 2023)
6-149572516-A-G		not specified	Uncertain significance (Aug 17, 2022)
6-149572550-A-G		not specified	Uncertain significance (Jan 18, 2023)
6-149572588-T-G		not specified	Uncertain significance (Aug 12, 2021)
6-149578869-A-G		not specified	Uncertain significance (Sep 01, 2021)
6-149578899-T-A		not specified	Uncertain significance (Dec 18, 2023)
6-149578914-G-C		not specified	Uncertain significance (Mar 17, 2023)
6-149579849-G-A		not specified	Uncertain significance (Feb 23, 2023)
6-149579862-A-T		not specified	Uncertain significance (Oct 26, 2022)
6-149579880-G-A		not specified	Likely benign (Apr 26, 2023)
6-149579904-A-G		not specified	Uncertain significance (Sep 06, 2022)
6-149579927-A-G		not specified	Uncertain significance (Dec 22, 2023)
6-149579936-T-C		not specified	Uncertain significance (Feb 28, 2024)
6-149579957-A-G		not specified	Uncertain significance (Jan 31, 2023)
6-149580658-G-A		not specified	Uncertain significance (May 31, 2022)
6-149582452-T-G		not specified	Uncertain significance (May 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GINM1	protein_coding	protein_coding	ENST00000367419	8	25455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.03e-9	0.222	125687	0	54	125741	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	129	167	0.771	0.00000781	2136
Missense in Polyphen		33	42.962	0.76813		628
Synonymous	0.777	54	61.8	0.874	0.00000297	638
Loss of Function	0.509	14	16.2	0.864	8.35e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000648	0.000645
Ashkenazi Jewish	0.00	0.00
East Asian	0.00130	0.00109
Finnish	0.0000935	0.0000924
European (Non-Finnish)	0.000121	0.0000879
Middle Eastern	0.00130	0.00109
South Asian	0.000316	0.000261
Other	0.000539	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.215
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ginm1

Gene ontology

• Cellular component: integral component of membrane