GINM1

protein-coding

glycosylated integral membrane protein 1

Gene summary

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf72

MANE transcript

NM_138785.5

Inheritance

—

ClinVar variants

U:45B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr6:149,566,294-149,591,748

External References & Databases

Ensembl (ENSG00000055211)

Transcript & Mutation Effects

hg38 • Region Span ~25.5 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 GINM1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138785.5. 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						0
missense			39 clinvar	2 clinvar		41
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	45	2	0	47

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138785.5	RefSeq	NP_620140.1	8	MANE Select
ENST00000367419.10	Ensembl	ENSP00000356389.5	8	MANE Select
ENST00000433539.1	Ensembl	ENSP00000407343.1	4	Standard
ENST00000650599.1	Ensembl	ENSP00000496902.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367419
Coding exons: 8
Length: 25455
Individuals with no LoFs: 125687
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 125741
p: 0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.05	129	167	0.771	0.00000781	2136
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00034	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0013	0.0011	notable
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00012	0.000088	rare
South Asian	0.00032	0.00026	rare
Other	0.00054	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.37
RVIS percentile EVS: 75.12

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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