GRAMD1A

protein-coding

GRAM domain containing 1A, 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 cholesterol transport. Located in endoplasmic reticulum membrane; organelle membrane contact site; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

KIAA1533

MANE transcript

NM_020895.5

Inheritance

—

ClinVar variants

U:117B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr19:34,994,784-35,026,471

External References & Databases

Ensembl (ENSG00000089351)

Transcript & Mutation Effects

hg38 • Region Span ~31.7 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 GRAMD1A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020895.5. 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			3 clinvar			3
missense			108 clinvar	4 clinvar		112
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	117	4	0	121

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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_020895.5	RefSeq	NP_065946.2	20	MANE Select
ENST00000317991.10	Ensembl	ENSP00000441032.1	20	MANE Select
NM_001136199.3	RefSeq	NP_001129671.1	18	Standard
NM_001320034.2	RefSeq	NP_001306963.1	19	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

integral component of membrane
intrinsic component of endoplasmic reticulum membrane
extrinsic component of cytoplasmic side of plasma membrane
organelle membrane contact site
endoplasmic reticulum-plasma membrane contact site

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317991
Coding exons: 20
Length: 31688
Individuals with no LoFs: 124344
Homozygous LoFs: 0
Heterozygous LoFs: 475
Defined: 124819
p: 0.00190

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.29	390	469	0.832	0.0000319	4682
Missense (PolyPhen)		71	87.881	0.80791		771
Synonymous	0.151	195	198	0.986	0.0000132	1476
Loss of Function	4.07	13	41.1	0.316	0.00000211	436

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00045	0.00045	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00017	0.00017	rare
Finnish	0.00093	0.00093	rare
European (Non-Finnish)	0.0030	0.0030	notable
South Asian	0.0018	0.0018	notable
Other	0.0017	0.0016	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in tumor progression. {ECO:0000269|PubMed:27585821}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.544
RVIS EVS: -1.02
RVIS percentile EVS: 8.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.572

Gene Damage Prediction

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