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.

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.

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			49	3		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	3	0

Variants in GRAMD1A

This is a list of pathogenic ClinVar variants found in the GRAMD1A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35009135-G-T		not specified	Uncertain significance (Jan 10, 2023)
19-35009136-G-A		not specified	Uncertain significance (Oct 17, 2023)
19-35009163-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-35009198-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-35009231-G-A		not specified	Uncertain significance (Mar 16, 2022)
19-35009274-C-G		not specified	Uncertain significance (Mar 28, 2024)
19-35009293-G-C		not specified	Uncertain significance (May 04, 2023)
19-35009307-G-A		not specified	Uncertain significance (Jan 16, 2024)
19-35009318-C-T		not specified	Uncertain significance (Aug 14, 2023)
19-35010092-A-T		not specified	Uncertain significance (Aug 12, 2024)
19-35010112-C-T		not specified	Uncertain significance (Nov 09, 2024)
19-35010330-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-35010343-C-G		not specified	Uncertain significance (Oct 27, 2022)
19-35011504-C-T		not specified	Uncertain significance (Jun 02, 2023)
19-35013268-C-T		not specified	Uncertain significance (Jan 26, 2023)
19-35013301-G-A		not specified	Uncertain significance (Nov 15, 2023)
19-35013350-T-C		not specified	Uncertain significance (Jan 02, 2024)
19-35013362-G-A		not specified	Uncertain significance (Aug 21, 2023)
19-35013543-C-G		not specified	Likely benign (Feb 23, 2023)
19-35013591-C-T		not specified	Uncertain significance (Jun 22, 2021)
19-35013606-G-A			Likely benign (Sep 01, 2023)
19-35013615-A-T		not specified	Uncertain significance (Oct 16, 2024)
19-35013657-A-G		not specified	Uncertain significance (Jan 30, 2024)
19-35013669-C-T		not specified	Uncertain significance (Aug 15, 2023)
19-35013677-G-A		not specified	Uncertain significance (Feb 22, 2023)

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