GRAMD1A

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

Basic information

Region (hg38): 19:34994784-35026471

Previous symbols: [ "KIAA1533" ]

Links

ENSG00000089351 ∙ NCBI:57655 ∙ OMIM:620178 ∙ HGNC:29305 ∙ Uniprot:Q96CP6 ∙ 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 GRAMD1A gene.

• not_specified (98 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRAMD1A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020895.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			96	3		99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	96	3	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRAMD1A	protein_coding	protein_coding	ENST00000317991	20	31688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00131	0.999	124344	0	475	124819	0.00190

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	390	469	0.832	0.0000319	4682
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00156	0.00156
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000167	0.000167
Finnish	0.000928	0.000928
European (Non-Finnish)	0.00303	0.00301
Middle Eastern	0.000167	0.000167
South Asian	0.00180	0.00180
Other	0.00165	0.00165

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.119
• hipred: Y
• hipred_score: 0.563
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.572

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gramd1a

Gene ontology

• Biological process: cholesterol transport;cellular response to cholesterol;intermembrane sterol transfer
• 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
• Molecular function: protein binding;cholesterol binding;intermembrane cholesterol transfer activity