SCRG1

stimulator of chondrogenesis 1

Basic information

Region (hg38): 4:173384700-173406380

Links

ENSG00000164106 ∙ NCBI:11341 ∙ OMIM:603163 ∙ HGNC:17036 ∙ Uniprot:O75711 ∙ 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 SCRG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCRG1 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in SCRG1

This is a list of pathogenic ClinVar variants found in the SCRG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-173388347-A-C		not specified	Uncertain significance (Nov 14, 2023)
4-173388351-T-C		not specified	Uncertain significance (Jan 03, 2024)
4-173388391-C-T		not specified	Likely benign (Jun 07, 2023)
4-173391291-G-A		not specified	Uncertain significance (Jan 30, 2024)
4-173391326-C-T		not specified	Uncertain significance (Mar 15, 2024)
4-173391363-C-A		not specified	Uncertain significance (Apr 04, 2023)
4-173391366-C-T		not specified	Uncertain significance (Aug 02, 2021)
4-173391386-A-G		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCRG1	protein_coding	protein_coding	ENST00000296506	2	21680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0445	0.684	125733	0	10	125743	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0199	53	52.6	1.01	0.00000277	654
Missense in Polyphen		15	21.521	0.69699		262
Synonymous	0.175	19	20.0	0.950	0.00000120	179
Loss of Function	0.561	2	3.06	0.654	1.28e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.737
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scrg1

Gene ontology

• Biological process: nervous system development
• Cellular component: extracellular space;Golgi apparatus;neuron projection terminus
• Molecular function: protein binding