GRAMD2B

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

Basic information

Region (hg38): 5:126360131-126496494

Previous symbols: [ "GRAMD3" ]

Links

ENSG00000155324 ∙ NCBI:65983 ∙ OMIM:620182 ∙ HGNC:24911 ∙ Uniprot:Q96HH9 ∙ 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 GRAMD2B gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRAMD2B 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in GRAMD2B

This is a list of pathogenic ClinVar variants found in the GRAMD2B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-126465443-G-C		not specified	Uncertain significance (Nov 14, 2023)
5-126465473-C-T		not specified	Uncertain significance (May 27, 2022)
5-126465479-C-G		not specified	Uncertain significance (Oct 03, 2023)
5-126465509-C-T		not specified	Uncertain significance (Jul 14, 2021)
5-126465510-G-A		not specified	Likely benign (Dec 27, 2023)
5-126469719-G-C		not specified	Uncertain significance (Sep 29, 2023)
5-126472289-G-A		not specified	Uncertain significance (Sep 29, 2023)
5-126480492-T-C		not specified	Uncertain significance (Dec 08, 2023)
5-126483463-G-T		not specified	Uncertain significance (Aug 01, 2022)
5-126483494-G-C		not specified	Uncertain significance (Jan 04, 2024)
5-126483517-G-A		not specified	Uncertain significance (Apr 25, 2023)
5-126483572-G-A		not specified	Uncertain significance (May 08, 2023)
5-126484495-A-C		not specified	Uncertain significance (Feb 13, 2024)
5-126485719-T-C		not specified	Uncertain significance (Jan 19, 2024)
5-126485737-C-T		not specified	Likely benign (Aug 10, 2023)
5-126486893-C-T		not specified	Uncertain significance (Jul 06, 2021)
5-126486955-A-G		not specified	Uncertain significance (Oct 20, 2021)
5-126486958-G-A		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRAMD2B	protein_coding	protein_coding	ENST00000513040	14	136363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.52e-12	0.246	125638	0	109	125747	0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	183	227	0.806	0.0000109	2920
Missense in Polyphen		49	62.656	0.78205		895
Synonymous	0.284	83	86.4	0.961	0.00000455	848
Loss of Function	0.989	21	26.5	0.793	0.00000127	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000588	0.000587
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000672	0.000668
Middle Eastern	0.000163	0.000163
South Asian	0.000360	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0978

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.216
• ghis: 0.544

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Gramd3

Gene ontology

• Cellular component: cytoplasmic microtubule
• Molecular function: protein binding;identical protein binding