GCSAML

germinal center associated signaling and motility like

Basic information

Region (hg38): 1:247507058-247577690

Previous symbols: [ "C1orf150" ]

Links

ENSG00000169224 ∙ NCBI:148823 ∙ ∙ HGNC:29583 ∙ Uniprot:Q5JQS6 ∙ 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 GCSAML gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCSAML 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			16			16
Total	0	0	24	0	0

Variants in GCSAML

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

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

Position	Type	Phenotype	Significance	ClinVar
1-247531599-T-C		not specified	Uncertain significance (Mar 29, 2023)
1-247531604-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-247531605-G-A		not specified	Uncertain significance (Nov 03, 2023)
1-247531658-G-A		not specified	Uncertain significance (Dec 15, 2023)
1-247531661-G-T		not specified	Uncertain significance (Sep 29, 2022)
1-247531772-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-247531904-G-C		not specified	Uncertain significance (Jun 06, 2023)
1-247531932-T-C		not specified	Uncertain significance (Dec 20, 2023)
1-247532027-G-C		not specified	Uncertain significance (Mar 07, 2023)
1-247532052-G-C		not specified	Uncertain significance (Oct 22, 2021)
1-247532144-C-T		not specified	Uncertain significance (Sep 25, 2023)
1-247532285-G-T		not specified	Uncertain significance (Mar 19, 2024)
1-247532342-T-C		not specified	Uncertain significance (Apr 12, 2023)
1-247532423-A-T		not specified	Uncertain significance (Jan 10, 2022)
1-247532424-T-C		not specified	Uncertain significance (Dec 17, 2023)
1-247532466-G-C		not specified	Uncertain significance (Mar 19, 2024)
1-247532493-C-T		not specified	Uncertain significance (Dec 16, 2023)
1-247532505-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-247556448-C-T		not specified	Uncertain significance (Feb 09, 2022)
1-247556456-G-A		not specified	Uncertain significance (Aug 05, 2021)
1-247563634-A-G		not specified	Uncertain significance (May 15, 2023)
1-247574169-A-C		not specified	Uncertain significance (Nov 27, 2023)
1-247574237-G-A		not specified	Uncertain significance (Dec 07, 2023)
1-247574312-T-C		not specified	Uncertain significance (May 26, 2024)
1-247574351-A-G		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCSAML	protein_coding	protein_coding	ENST00000366488	5	70633

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.125	0.788	113399	434	11907	125740	0.0503

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.311	73	65.9	1.11	0.00000308	887
Missense in Polyphen		16	16.205	0.98733		221
Synonymous	1.43	15	23.9	0.628	0.00000113	235
Loss of Function	1.37	2	5.44	0.368	3.12e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0646	0.0639
Ashkenazi Jewish	0.104	0.101
East Asian	0.0248	0.0241
Finnish	0.0530	0.0522
European (Non-Finnish)	0.0663	0.0640
Middle Eastern	0.0248	0.0241
South Asian	0.0299	0.0291
Other	0.0605	0.0587

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.11

Haploinsufficiency Scores

• pHI: 0.0820
• hipred: N
• hipred_score: 0.123
• ghis: 0.452

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

Gene ontology

• Biological process: regulation of B cell receptor signaling pathway;regulation of lymphocyte migration