GRAMD1B

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

Basic information

Region (hg38): 11:123358428-123627774

Previous symbols: [ "LINC01059" ]

Links

ENSG00000023171 ∙ NCBI:57476 ∙ OMIM:620179 ∙ HGNC:29214 ∙ Uniprot:Q3KR37 ∙ 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 GRAMD1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRAMD1B 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				4	3	7
missense			29	6	2	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding					1	1
Total	0	0	29	10	6

Variants in GRAMD1B

This is a list of pathogenic ClinVar variants found in the GRAMD1B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-123577386-C-G		not specified	Uncertain significance (Dec 19, 2023)
11-123577489-C-G		not specified	Uncertain significance (May 31, 2023)
11-123577563-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-123584304-C-T		GRAMD1B-related disorder	Likely benign (Aug 07, 2019)
11-123594078-G-A		GRAMD1B-related disorder	Benign (Jun 11, 2019)
11-123594776-C-T		Intellectual disability	Likely pathogenic (-)
11-123595994-G-T		not specified	Uncertain significance (Aug 04, 2021)
11-123603537-A-G		not specified	Uncertain significance (Jul 20, 2022)
11-123605357-T-C		not specified	Uncertain significance (Apr 11, 2023)
11-123605383-A-G		not specified	Uncertain significance (Apr 15, 2024)
11-123605400-T-A			Benign (Aug 08, 2017)
11-123605469-C-T			Benign (Jan 05, 2018)
11-123606637-C-T		not specified	Likely benign (May 06, 2024)
11-123606644-G-A		GRAMD1B-related disorder	Benign (Oct 21, 2019)
11-123606648-G-T		not specified	Uncertain significance (Oct 05, 2022)
11-123606661-A-G		not specified	Uncertain significance (May 24, 2023)
11-123606672-G-A		not specified	Uncertain significance (Dec 16, 2021)
11-123606675-A-G			Likely benign (May 01, 2023)
11-123606682-A-G		GRAMD1B-related disorder	Likely benign (Jun 24, 2019)
11-123606742-A-G		not specified	Uncertain significance (Feb 23, 2023)
11-123606750-G-A		not specified	Uncertain significance (May 11, 2022)
11-123608664-G-A		GRAMD1B-related disorder	Likely benign (Aug 11, 2022)
11-123608758-A-G		not specified	Uncertain significance (Jun 10, 2024)
11-123608773-G-A		not specified	Uncertain significance (Oct 30, 2023)
11-123608775-G-A		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRAMD1B	protein_coding	protein_coding	ENST00000529750	20	102139

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000713	124629	0	9	124638	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.23	249	440	0.566	0.0000270	4838
Missense in Polyphen		60	149.89	0.4003		1584
Synonymous	-0.0143	176	176	1.00	0.0000120	1314
Loss of Function	5.37	5	43.0	0.116	0.00000217	488

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000137	0.000129
Ashkenazi Jewish	0.000104	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000447	0.0000442
Middle Eastern	0.00	0.00
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ectoderm Differentiation (Consensus)

Intolerance Scores

• loftool: 0.353
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.51

Haploinsufficiency Scores

• pHI: 0.393
• hipred: Y
• hipred_score: 0.755
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.169

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gramd1b

Gene ontology

• Biological process: cholesterol transport;cholesterol homeostasis;cellular response to cholesterol;intermembrane sterol transfer
• Cellular component: endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane;endoplasmic reticulum-plasma membrane contact site
• Molecular function: phosphatidylserine binding;cholesterol binding;phosphatidic acid binding;intermembrane cholesterol transfer activity