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.

• not_specified (41 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_001012642.3. 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			39	2		41
nonsense						0
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	3	0

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