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.

• not_specified (13 variants)

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. These statistics are base on transcript: NM_000145278.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			13			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	0	0

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