GRAMD4

GRAM domain containing 4, the group of GRAM domain containing

Basic information

Region (hg38): 22:46576012-46679790

Links

ENSG00000075240 ∙ NCBI:23151 ∙ OMIM:613691 ∙ HGNC:29113 ∙ Uniprot:Q6IC98 ∙ 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 GRAMD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRAMD4 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			46	2	1	49
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	2	1

Variants in GRAMD4

This is a list of pathogenic ClinVar variants found in the GRAMD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-46626836-C-T		not specified	Uncertain significance (Oct 25, 2022)
22-46626857-G-C		not specified	Uncertain significance (Sep 26, 2023)
22-46626857-G-T		not specified	Uncertain significance (Dec 13, 2024)
22-46626905-A-G		not specified	Uncertain significance (Apr 08, 2024)
22-46626916-G-C		not specified	Uncertain significance (Mar 08, 2025)
22-46626917-G-A		not specified	Likely benign (Aug 12, 2021)
22-46626917-G-T			Benign (Mar 29, 2018)
22-46626932-C-A		not specified	Uncertain significance (Aug 04, 2022)
22-46626936-G-C		not specified	Uncertain significance (Aug 02, 2023)
22-46626940-C-A		not specified	Uncertain significance (Jul 27, 2024)
22-46626940-C-G		not specified	Uncertain significance (Mar 18, 2024)
22-46626941-A-G		not specified	Uncertain significance (Sep 09, 2024)
22-46626944-G-A		not specified	Uncertain significance (Oct 05, 2021)
22-46637879-G-C		not specified	Uncertain significance (Aug 14, 2023)
22-46658199-G-A		not specified	Uncertain significance (Aug 11, 2022)
22-46658220-A-G		not specified	Uncertain significance (Mar 19, 2024)
22-46658222-G-A		not specified	Uncertain significance (Jun 16, 2022)
22-46658223-C-T		not specified	Uncertain significance (Dec 24, 2024)
22-46658255-C-T		not specified	Uncertain significance (Sep 10, 2024)
22-46658259-A-G		not specified	Uncertain significance (Dec 16, 2022)
22-46658294-G-T		not specified	Uncertain significance (Nov 14, 2023)
22-46661392-A-G		not specified	Uncertain significance (Aug 05, 2024)
22-46663045-C-T		not specified	Uncertain significance (Dec 01, 2022)
22-46663064-C-G		not specified	Uncertain significance (Dec 20, 2022)
22-46663066-C-T		not specified	Uncertain significance (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRAMD4	protein_coding	protein_coding	ENST00000406902	18	103780

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000239	125732	0	3	125735	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	249	391	0.636	0.0000271	3771
Missense in Polyphen		58	133.02	0.43603		1274
Synonymous	0.0182	171	171	0.998	0.0000131	1110
Loss of Function	5.48	2	38.8	0.0515	0.00000210	407

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000886	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as a mediator of E2F1-induced apoptosis in the absence of p53/TP53. {ECO:0000269|PubMed:15565177}.
• Pathway: p73 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.0264
• rvis_EVS: -1.07
• rvis_percentile_EVS: 7.43

Haploinsufficiency Scores

• pHI: 0.119
• hipred: Y
• hipred_score: 0.662
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.584

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gramd4

Gene ontology

• Biological process: apoptotic process;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
• Cellular component: mitochondrion;integral component of membrane;mitochondrial membrane
• Molecular function: molecular_function