GUCA1C

guanylate cyclase activator 1C, the group of EF-hand domain containing

Basic information

Region (hg38): 3:108907792-108953879

Links

ENSG00000138472 ∙ NCBI:9626 ∙ OMIM:605128 ∙ HGNC:4680 ∙ Uniprot:O95843 ∙ 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 GUCA1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GUCA1C 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in GUCA1C

This is a list of pathogenic ClinVar variants found in the GUCA1C region.

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

Position	Type	Phenotype	Significance	ClinVar
3-108908042-C-T		not specified	Uncertain significance (Sep 26, 2022)
3-108908098-C-G		not specified	Uncertain significance (Nov 15, 2021)
3-108908148-A-C		not specified	Uncertain significance (Dec 01, 2022)
3-108908195-C-G		not specified	Uncertain significance (Feb 21, 2024)
3-108908201-T-G		not specified	Uncertain significance (Mar 02, 2023)
3-108916159-A-G		not specified	Uncertain significance (Mar 12, 2024)
3-108920452-A-C		not specified	Uncertain significance (Jan 03, 2024)
3-108920461-T-C		not specified	Uncertain significance (Jul 25, 2023)
3-108920518-T-A		not specified	Uncertain significance (Feb 28, 2023)
3-108920518-T-C		not specified	Uncertain significance (Jul 19, 2022)
3-108920528-T-G		not specified	Uncertain significance (Jul 19, 2023)
3-108920536-A-C		not specified	Uncertain significance (May 04, 2022)
3-108920575-A-G		not specified	Uncertain significance (Aug 28, 2021)
3-108953566-G-A		not specified	Likely benign (Dec 21, 2021)
3-108953720-G-T		not specified	Uncertain significance (Jun 30, 2023)
3-108953726-C-T		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GUCA1C	protein_coding	protein_coding	ENST00000261047	4	46104

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.57e-7	0.0907	62931	11564	51215	125710	0.292

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.317	116	107	1.09	0.00000484	1413
Missense in Polyphen		24	22.199	1.0811		324
Synonymous	0.763	33	39.1	0.845	0.00000189	361
Loss of Function	-0.669	9	7.08	1.27	3.00e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.607	0.606
Ashkenazi Jewish	0.223	0.221
East Asian	0.157	0.157
Finnish	0.330	0.329
European (Non-Finnish)	0.325	0.323
Middle Eastern	0.157	0.157
South Asian	0.240	0.236
Other	0.298	0.299

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulates guanylyl cyclase 1 (GC1) and GC2 when free calcium ions concentration is low and inhibits guanylyl cyclases when free calcium ions concentration is elevated. This Ca(2+)- sensitive regulation of guanylyl cyclase (GC) is a key event in recovery of the dark state of rod photoreceptors following light exposure.
• Pathway: Phototransduction - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Visual signal transduction: Rods;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling;Visual signal transduction: Cones (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.698
• rvis_EVS: 0.99
• rvis_percentile_EVS: 90.56

Haploinsufficiency Scores

• pHI: 0.0467
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0242

Gene Damage Prediction

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

Gene ontology

• Biological process: signal transduction;visual perception;regulation of rhodopsin mediated signaling pathway;positive regulation of guanylate cyclase activity
• Cellular component: photoreceptor disc membrane
• Molecular function: calcium ion binding;calcium sensitive guanylate cyclase activator activity