GRAMD2A

GRAM domain containing 2A, the group of GRAM domain containing

Basic information

Region (hg38): 15:72159806-72197787

Previous symbols: [ "GRAMD2" ]

Links

ENSG00000175318 ∙ NCBI:196996 ∙ OMIM:620181 ∙ HGNC:27287 ∙ Uniprot:Q8IUY3 ∙ 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 GRAMD2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRAMD2A 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			26	2		28
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	0

Variants in GRAMD2A

This is a list of pathogenic ClinVar variants found in the GRAMD2A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-72162291-T-C		not specified	Likely benign (Oct 12, 2022)
15-72162295-C-T		not specified	Likely benign (Oct 07, 2024)
15-72162342-G-A		not specified	Uncertain significance (Jan 04, 2024)
15-72162361-T-C		not specified	Uncertain significance (Jan 26, 2023)
15-72163291-G-A		not specified	Uncertain significance (Aug 21, 2024)
15-72163315-C-T		not specified	Uncertain significance (Oct 20, 2023)
15-72163317-G-A		not specified	Uncertain significance (Oct 26, 2024)
15-72163319-G-C		not specified	Uncertain significance (Aug 17, 2021)
15-72163386-G-A		not specified	Uncertain significance (Nov 19, 2024)
15-72163398-G-C		not specified	Uncertain significance (Apr 23, 2024)
15-72163417-C-A		not specified	Uncertain significance (Mar 07, 2025)
15-72163444-C-A		not specified	Uncertain significance (Mar 29, 2023)
15-72163621-G-A		not specified	Uncertain significance (Nov 15, 2024)
15-72163644-ACTGT-A			Likely benign (Dec 31, 2019)
15-72163705-G-T		not specified	Uncertain significance (Nov 15, 2024)
15-72166649-C-G		not specified	Uncertain significance (Dec 21, 2022)
15-72166679-G-A		not specified	Uncertain significance (May 20, 2024)
15-72167025-C-T		not specified	Uncertain significance (Jan 17, 2025)
15-72167049-T-C		not specified	Uncertain significance (Dec 13, 2021)
15-72167756-G-C		not specified	Uncertain significance (Apr 04, 2023)
15-72167782-G-C		not specified	Uncertain significance (Dec 18, 2023)
15-72167792-A-T		not specified	Uncertain significance (Jun 26, 2024)
15-72167795-G-C		not specified	Uncertain significance (Nov 17, 2022)
15-72167797-C-T		not specified	Uncertain significance (Mar 19, 2024)
15-72168511-A-C		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRAMD2A	protein_coding	protein_coding	ENST00000309731	12	37979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.49e-13	0.0438	125305	1	442	125748	0.00176

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.959	149	186	0.802	0.00000945	2303
Missense in Polyphen		51	68.612	0.74332		824
Synonymous	1.41	55	70.0	0.786	0.00000329	664
Loss of Function	0.281	20	21.4	0.934	9.92e-7	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00115
Ashkenazi Jewish	0.00	0.00
East Asian	0.00163	0.00163
Finnish	0.00107	0.00106
European (Non-Finnish)	0.00292	0.00283
Middle Eastern	0.00163	0.00163
South Asian	0.000866	0.000850
Other	0.00253	0.00245

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.0475
• hipred: N
• hipred_score: 0.144
• ghis: 0.428

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Gramd2

Gene ontology

• Biological process: endoplasmic reticulum-plasma membrane tethering;regulation of store-operated calcium entry
• Cellular component: integral component of membrane;intrinsic component of endoplasmic reticulum membrane;extrinsic component of cytoplasmic side of plasma membrane;organelle membrane contact site
• Molecular function: phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol binding