GSG1

germ cell associated 1

Basic information

Region (hg38): 12:13083532-13103683

Links

ENSG00000111305 ∙ NCBI:83445 ∙ ∙ HGNC:19716 ∙ Uniprot:Q2KHT4 ∙ 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 GSG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GSG1 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				1		1
missense			28	6		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	7	0

Variants in GSG1

This is a list of pathogenic ClinVar variants found in the GSG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-13084953-C-A		not specified	Uncertain significance (Jun 28, 2024)
12-13084974-T-C		not specified	Uncertain significance (Aug 15, 2023)
12-13084988-G-A		not specified	Likely benign (Dec 13, 2023)
12-13085044-G-A		not specified	Uncertain significance (Oct 04, 2022)
12-13085088-C-T		not specified	Likely benign (Dec 08, 2023)
12-13085089-G-A		not specified	Uncertain significance (Sep 01, 2021)
12-13085091-C-T		not specified	Likely benign (Apr 22, 2022)
12-13085130-T-C		not specified	Uncertain significance (Apr 07, 2022)
12-13085187-G-A		not specified	Uncertain significance (Jan 17, 2025)
12-13085208-G-A		not specified	Uncertain significance (May 23, 2023)
12-13087209-A-G		not specified	Likely benign (Oct 20, 2023)
12-13087210-C-T		not specified	Uncertain significance (Feb 21, 2024)
12-13087211-A-G		not specified	Likely benign (Oct 01, 2024)
12-13087927-G-T		not specified	Uncertain significance (Jan 23, 2025)
12-13087937-C-T		not specified	Uncertain significance (Jan 29, 2025)
12-13087955-A-G		not specified	Uncertain significance (Jun 07, 2024)
12-13087958-C-T		not specified	Uncertain significance (Jul 09, 2021)
12-13088018-C-T		not specified	Uncertain significance (Nov 09, 2024)
12-13088023-T-C		not specified	Uncertain significance (Jun 05, 2024)
12-13088034-C-T		not specified	Likely benign (Feb 06, 2024)
12-13088035-G-A		not specified	Uncertain significance (Aug 21, 2023)
12-13088053-A-G		not specified	Uncertain significance (May 31, 2023)
12-13088879-G-A		not specified	Uncertain significance (May 03, 2023)
12-13088897-C-T		not specified	Uncertain significance (Jul 31, 2024)
12-13089216-G-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GSG1	protein_coding	protein_coding	ENST00000432710	6	20126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00104	0.954	124772	4	968	125744	0.00387

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.224	184	193	0.955	0.0000105	2206
Missense in Polyphen		53	58.342	0.90844		741
Synonymous	0.351	76	80.0	0.950	0.00000460	677
Loss of Function	1.77	7	14.2	0.494	6.90e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00274	0.00274
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.00	0.00
Finnish	0.00310	0.00310
European (Non-Finnish)	0.00632	0.00630
Middle Eastern	0.00	0.00
South Asian	0.00216	0.00216
Other	0.00489	0.00490

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May cause the redistribution of PAPOLB from the cytosol to the endoplasmic reticulum. {ECO:0000250}.

Intolerance Scores

• loftool: 0.920
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.58

Haploinsufficiency Scores

• pHI: 0.0552
• hipred: N
• hipred_score: 0.190

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.170

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gsg1

Gene ontology

• Cellular component: endoplasmic reticulum membrane;plasma membrane;integral component of membrane
• Molecular function: protein binding;RNA polymerase binding