GRAMD1C

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

Basic information

Region (hg38): 3:113828181-113947174

Links

ENSG00000178075 ∙ NCBI:54762 ∙ OMIM:620180 ∙ HGNC:25252 ∙ Uniprot:Q8IYS0 ∙ 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 GRAMD1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRAMD1C 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			29	3		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	0

Variants in GRAMD1C

This is a list of pathogenic ClinVar variants found in the GRAMD1C region.

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

Position	Type	Phenotype	Significance	ClinVar
3-113838923-C-G		not specified	Uncertain significance (Oct 20, 2023)
3-113838923-C-T		not specified	Likely benign (Dec 07, 2021)
3-113838931-C-A		not specified	Uncertain significance (Dec 27, 2022)
3-113844513-A-G		not specified	Uncertain significance (Dec 13, 2023)
3-113844566-A-T		not specified	Uncertain significance (Nov 04, 2022)
3-113844569-C-T		not specified	Uncertain significance (Jun 13, 2024)
3-113844603-A-C		not specified	Uncertain significance (Feb 09, 2022)
3-113844621-A-G		not specified	Uncertain significance (Aug 16, 2021)
3-113875526-G-A		not specified	Uncertain significance (May 17, 2023)
3-113875575-A-T		not specified	Uncertain significance (Aug 28, 2023)
3-113876219-C-T		not specified	Uncertain significance (May 18, 2022)
3-113876246-A-G		not specified	Uncertain significance (May 20, 2024)
3-113882818-G-A		not specified	Uncertain significance (Nov 22, 2023)
3-113901105-G-C		not specified	Uncertain significance (Jan 26, 2022)
3-113901125-C-T		not specified	Uncertain significance (Sep 16, 2021)
3-113904166-A-T		not specified	Uncertain significance (Oct 24, 2023)
3-113904244-A-C		not specified	Uncertain significance (Jun 04, 2024)
3-113904252-G-A		not specified	Uncertain significance (Mar 05, 2024)
3-113908965-G-A		not specified	Uncertain significance (Mar 31, 2024)
3-113909012-C-T		not specified	Uncertain significance (May 09, 2024)
3-113915719-A-G		not specified	Uncertain significance (Jan 03, 2024)
3-113915720-T-G		not specified	Uncertain significance (Dec 08, 2023)
3-113915745-C-T		not specified	Uncertain significance (Mar 28, 2024)
3-113915746-G-A		not specified	Uncertain significance (May 24, 2024)
3-113915770-G-A		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRAMD1C	protein_coding	protein_coding	ENST00000358160	18	118993

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.63e-21	0.0405	125497	0	251	125748	0.000999

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.843	288	331	0.870	0.0000163	4306
Missense in Polyphen		71	84.069	0.84454		1161
Synonymous	1.34	99	118	0.842	0.00000558	1195
Loss of Function	1.14	36	44.2	0.815	0.00000258	518

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00653	0.00649
Ashkenazi Jewish	0.000111	0.0000992
East Asian	0.000768	0.000761
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000920	0.000906
Middle Eastern	0.000768	0.000761
South Asian	0.000366	0.000359
Other	0.000657	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.972
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.57

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.253
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.317

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gramd1c

Gene ontology

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