GSTCD

glutathione S-transferase C-terminal domain containing, the group of 7BS orphan methyltransferases

Basic information

Region (hg38): 4:105708778-105847725

Links

ENSG00000138780 ∙ NCBI:79807 ∙ OMIM:615912 ∙ HGNC:25806 ∙ Uniprot:Q8NEC7 ∙ 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 GSTCD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSTCD 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in GSTCD

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

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

Position	Type	Phenotype	Significance	ClinVar
4-105717756-T-C		not specified	Uncertain significance (Oct 26, 2022)
4-105717789-A-G		not specified	Uncertain significance (Mar 17, 2023)
4-105717887-G-A		not specified	Uncertain significance (Nov 02, 2023)
4-105717909-A-G		not specified	Uncertain significance (Mar 20, 2023)
4-105717973-C-A		not specified	Uncertain significance (Jan 31, 2024)
4-105717986-G-C		not specified	Uncertain significance (May 09, 2022)
4-105719144-A-G		not specified	Likely benign (Nov 21, 2022)
4-105719190-C-T		not specified	Uncertain significance (Jan 26, 2022)
4-105719198-G-A		not specified	Uncertain significance (Jul 12, 2023)
4-105719219-C-T		not specified	Uncertain significance (Feb 16, 2023)
4-105719232-T-G		not specified	Uncertain significance (Mar 02, 2023)
4-105719345-G-A		not specified	Uncertain significance (Jul 19, 2023)
4-105719403-G-A		not specified	Uncertain significance (May 29, 2024)
4-105719447-C-G		not specified	Uncertain significance (Jun 21, 2023)
4-105726772-A-G		not specified	Uncertain significance (Feb 22, 2023)
4-105729426-G-A		not specified	Uncertain significance (Jun 29, 2023)
4-105822972-G-A		not specified	Uncertain significance (Mar 29, 2024)
4-105823264-C-T		not specified	Uncertain significance (Sep 01, 2021)
4-105825723-A-G		not specified	Uncertain significance (Sep 14, 2022)
4-105834477-G-T		not specified	Uncertain significance (Mar 22, 2023)
4-105834576-A-G		not specified	Uncertain significance (Jan 10, 2023)
4-105834582-A-G		not specified	Uncertain significance (Mar 29, 2022)
4-105845549-A-G		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSTCD	protein_coding	protein_coding	ENST00000515279	11	138951

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.42e-7	0.990	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.345	304	321	0.946	0.0000150	4149
Missense in Polyphen		118	125.41	0.94091		1582
Synonymous	-0.340	118	113	1.04	0.00000524	1203
Loss of Function	2.36	16	30.0	0.534	0.00000153	388

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000417
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000167	0.000163
South Asian	0.000410	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.949

Intolerance Scores

• loftool: 0.202
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.246
• hipred: N
• hipred_score: 0.291
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.466

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gstcd
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; hearing/vestibular/ear phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: nucleus;nucleoplasm;cytoplasm;extracellular exosome
• Molecular function: molecular_function;protein binding