CSH1

chorionic somatomammotropin hormone 1, the group of Growth hormone family

Basic information

Region (hg38): 17:63894909-63896661

Links

ENSG00000136488 ∙ NCBI:1442 ∙ OMIM:150200 ∙ HGNC:2440 ∙ Uniprot:P0DML2 ∙ 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 CSH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSH1 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in CSH1

This is a list of pathogenic ClinVar variants found in the CSH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63895066-G-T		not specified	Uncertain significance (Nov 10, 2023)
17-63895108-A-G		not specified	Likely benign (Apr 17, 2024)
17-63895132-G-C		not specified	Uncertain significance (Jan 23, 2024)
17-63895138-C-G		not specified	Uncertain significance (May 31, 2023)
17-63895140-T-C		not specified	Uncertain significance (Oct 10, 2023)
17-63895150-A-G		not specified	Uncertain significance (Oct 10, 2023)
17-63895161-A-G		not specified	Uncertain significance (Sep 06, 2022)
17-63895185-A-G		not specified	Uncertain significance (Oct 26, 2022)
17-63895198-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-63895200-C-T		not specified	Uncertain significance (Aug 01, 2022)
17-63895497-C-G		not specified	Uncertain significance (Jul 28, 2021)
17-63895526-C-T		not specified	Uncertain significance (Nov 18, 2022)
17-63895559-C-T		not specified	Likely benign (Nov 14, 2023)
17-63895563-C-G		not specified	Uncertain significance (Nov 14, 2023)
17-63895564-A-G		not specified	Uncertain significance (Nov 14, 2023)
17-63895591-A-C		not specified	Uncertain significance (Sep 14, 2021)
17-63895595-A-G		not specified	Uncertain significance (Nov 14, 2023)
17-63895618-A-G		not specified	Uncertain significance (Sep 16, 2021)
17-63896129-A-G			Likely benign (Aug 01, 2022)
17-63896132-G-C		not specified	Uncertain significance (Aug 09, 2021)
17-63896134-G-C		not specified	Uncertain significance (Aug 09, 2021)
17-63896135-G-T		not specified	Uncertain significance (Aug 09, 2021)
17-63896508-C-T		not specified	Uncertain significance (Jun 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSH1	protein_coding	protein_coding	ENST00000316193	5	1747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000213	0.297	125685	1	14	125700	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.595	129	111	1.16	0.00000734	1412
Missense in Polyphen		24	26.789	0.89587		459
Synonymous	-0.830	59	51.4	1.15	0.00000372	421
Loss of Function	-0.0360	7	6.90	1.01	3.39e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000770	0.000766
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Produced only during pregnancy and is involved in stimulating lactation, fetal growth and metabolism. Does not interact with GHR but only activates PRLR through zinc-induced dimerization. {ECO:0000269|PubMed:16546209}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;mtor signaling pathway;trefoil factors initiate mucosal healing;regulation of eif-4e and p70s6 kinase;Growth hormone receptor signaling;akt signaling pathway;Prolactin receptor signaling;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Growth hormone signaling;Immune System;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;growth hormone signaling pathway;GPCR signaling-G alpha i (Consensus)

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.318
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.145

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 signaling receptor activity;response to nutrient levels;positive regulation of tyrosine phosphorylation of STAT protein;positive regulation of growth;positive regulation of JAK-STAT cascade;animal organ development;positive regulation of peptidyl-tyrosine phosphorylation;growth hormone receptor signaling pathway;JAK-STAT cascade involved in growth hormone signaling pathway
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum;endosome lumen;vesicle
• Molecular function: growth hormone receptor binding;hormone activity;protein binding;growth factor activity;metal ion binding