GRAMD1C

protein-coding

GRAM domain containing 1C, the group of GRAM domain containing

Gene summary

Predicted to enable cholesterol binding activity and cholesterol transfer activity. Predicted to be involved in cellular response to cholesterol and intracellular sterol transport. Predicted to be located in membrane and organelle membrane contact site. Predicted to be active in endoplasmic reticulum membrane; endoplasmic reticulum-plasma membrane contact site; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_017577.5

Inheritance

—

ClinVar variants

U:87B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr3:113,828,182-113,947,174

External References & Databases

Ensembl (ENSG00000178075)

Transcript & Mutation Effects

hg38 • Region Span ~119.0 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 GRAMD1C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 81

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017577.5. 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			80 clinvar	5 clinvar		85
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	87	5	0	92

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017577.5	RefSeq	NP_060047.3	18	MANE Select
ENST00000358160.9	Ensembl	ENSP00000350881.4	18	MANE Select
NM_001172105.2	RefSeq	NP_001165576.1	12	Standard
ENST00000440446.2	Ensembl	ENSP00000408135.2	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cholesterol transport
cellular response to cholesterol
intermembrane sterol transfer

Molecular Function

protein binding
cholesterol binding
intermembrane cholesterol transfer activity

Cellular Component

endoplasmic reticulum membrane
plasma membrane
integral component of membrane
endoplasmic reticulum-plasma membrane contact site

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358160
Coding exons: 18
Length: 118993
Individuals with no LoFs: 125497
Homozygous LoFs: 0
Heterozygous LoFs: 251
Defined: 125748
p: 0.000999

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.843	288	331	0.870	0.0000163	4306
Missense (PolyPhen)		71	84.069	0.84454		1161
Synonymous	1.34	99	118	0.842	0.00000558	1195
Loss of Function	1.14	36	44.2	0.815	0.00000258	518

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0059	0.0059	notable
Latino/Admixed American	0.00063	0.00061	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00077	0.00076	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00092	0.00091	rare
South Asian	0.00037	0.00036	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.972
RVIS EVS: 0.13
RVIS percentile EVS: 63.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.317

Gene Damage Prediction

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