SCGB1C1

secretoglobin family 1C member 1, the group of Secretoglobins

Basic information

Region (hg38): 11:193077-194575

Links

ENSG00000188076 ∙ NCBI:147199 ∙ OMIM:610176 ∙ HGNC:18394 ∙ Uniprot:Q8TD33 ∙ 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 SCGB1C1 gene.

• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB1C1 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	2
missense					1	1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	2

Variants in SCGB1C1

This is a list of pathogenic ClinVar variants found in the SCGB1C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-193112-C-T			Benign (Aug 29, 2018)
11-193722-A-G			Benign (Aug 29, 2018)
11-193863-T-C			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGB1C1	protein_coding	protein_coding	ENST00000342878	3	1494

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000215	0.166	123578	0	26	123604	0.000105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0547	45	44.0	1.02	0.00000215	561
Missense in Polyphen		18	12.966	1.3883		195
Synonymous	0.0544	18	18.3	0.984	0.00000111	161
Loss of Function	-0.888	6	4.07	1.48	2.72e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000575	0.000574
Ashkenazi Jewish	0.00	0.00
East Asian	0.000389	0.000389
Finnish	0.00	0.00
European (Non-Finnish)	0.0000813	0.0000812
Middle Eastern	0.000389	0.000389
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0862

Intolerance Scores

• loftool: 0.544
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.208

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scgb1c1

Gene ontology

• Cellular component: extracellular region