GCSAM

germinal center associated signaling and motility

Basic information

Region (hg38): 3:112120839-112133270

Previous symbols: [ "GCET2" ]

Links

ENSG00000174500 ∙ NCBI:257144 ∙ OMIM:607792 ∙ HGNC:20253 ∙ Uniprot:Q8N6F7 ∙ 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 GCSAM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCSAM 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in GCSAM

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

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

Position	Type	Phenotype	Significance	ClinVar
3-112123498-C-T		not specified	Likely benign (Mar 15, 2024)
3-112123499-G-A		not specified	Uncertain significance (Apr 07, 2022)
3-112123514-A-G		not specified	Uncertain significance (Apr 24, 2024)
3-112123550-A-T		not specified	Uncertain significance (Feb 12, 2024)
3-112123556-C-T		not specified	Uncertain significance (Nov 09, 2024)
3-112123565-A-T		not specified	Uncertain significance (Apr 08, 2024)
3-112123586-T-C		not specified	Uncertain significance (Oct 30, 2023)
3-112123594-A-G		not specified	Uncertain significance (Nov 07, 2024)
3-112123645-C-G		not specified	Uncertain significance (Nov 22, 2021)
3-112123718-G-A		not specified	Uncertain significance (Mar 25, 2024)
3-112123724-T-C		not specified	Uncertain significance (Oct 24, 2024)
3-112123754-A-C		not specified	Uncertain significance (Jun 28, 2023)
3-112125234-G-T		not specified	Uncertain significance (Dec 27, 2022)
3-112127027-T-A		not specified	Uncertain significance (Aug 28, 2023)
3-112128042-C-T		not specified	Uncertain significance (Jul 25, 2023)
3-112130471-C-T		not specified	Uncertain significance (Oct 05, 2023)
3-112130512-G-A		not specified	Likely benign (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCSAM	protein_coding	protein_coding	ENST00000484193	6	12465

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0640	0.877	125669	0	10	125679	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.491	83	96.6	0.859	0.00000485	1182
Missense in Polyphen		33	37.956	0.86942		506
Synonymous	-0.275	33	31.0	1.06	0.00000142	322
Loss of Function	1.59	3	7.78	0.385	3.31e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000179	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the negative regulation of lymphocyte motility. It mediates the migration-inhibitory effects of IL6. Serves as a positive regulator of the RhoA signaling pathway. Enhancement of RhoA activation results in inhibition of lymphocyte and lymphoma cell motility by activation of its downstream effector ROCK. Is a regulator of B-cell receptor signaling, that acts through SYK kinase activation. {ECO:0000269|PubMed:17823310, ECO:0000269|PubMed:20844236, ECO:0000269|PubMed:23299888}.

Recessive Scores

• pRec: 0.0733

Intolerance Scores

• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.0302
• hipred: N
• hipred_score: 0.172
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gcsam
• Phenotype: immune system phenotype

Gene ontology

• Biological process: regulation of B cell receptor signaling pathway;negative regulation of lymphocyte migration
• Cellular component: cytoplasm;plasma membrane
• Molecular function: actin binding;protein binding;protein kinase binding;myosin II binding