CSH2

chorionic somatomammotropin hormone 2, the group of Growth hormone family

Basic information

Region (hg38): 17:63872012-63873766

Links

ENSG00000213218 ∙ NCBI:1443 ∙ OMIM:118820 ∙ HGNC:2441 ∙ Uniprot:P0DML3 ∙ 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 CSH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSH2 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	16	2	0

Variants in CSH2

This is a list of pathogenic ClinVar variants found in the CSH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63872128-A-G			Benign (Aug 15, 2018)
17-63872139-C-G		not specified	Uncertain significance (Oct 03, 2023)
17-63872154-C-A		not specified	Uncertain significance (Mar 22, 2023)
17-63872165-C-G		not specified	Likely benign (May 14, 2024)
17-63872165-C-T		not specified	Likely benign (Mar 30, 2024)
17-63872184-A-C		not specified	Uncertain significance (Apr 23, 2024)
17-63872301-C-T		not specified	Uncertain significance (Mar 31, 2024)
17-63872302-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-63872305-G-A		not specified	Uncertain significance (Jun 29, 2023)
17-63872597-C-T		not specified	Uncertain significance (Dec 27, 2022)
17-63872630-C-T		not specified	Likely benign (Sep 01, 2021)
17-63872633-T-A		not specified	Uncertain significance (Jun 29, 2022)
17-63872686-A-C		not specified	Uncertain significance (Aug 12, 2021)
17-63872695-A-C		not specified	Uncertain significance (Jun 11, 2021)
17-63872696-G-C		not specified	Uncertain significance (Sep 15, 2021)
17-63872726-G-A		not specified	Uncertain significance (Jun 11, 2021)
17-63872867-G-A		not specified	Uncertain significance (Aug 23, 2021)
17-63872872-G-A		not specified	Uncertain significance (Feb 03, 2022)
17-63873209-G-T		not specified	Uncertain significance (Apr 25, 2022)
17-63873213-G-A		not specified	Uncertain significance (Jul 29, 2023)
17-63873262-C-T		not specified	Uncertain significance (Sep 29, 2022)
17-63873277-C-G		not specified	Uncertain significance (Aug 13, 2021)
17-63873333-C-T		not specified	Likely benign (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSH2	protein_coding	protein_coding	ENST00000392886	5	1755

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0132	0.872	125676	1	67	125744	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.868	140	114	1.23	0.00000737	1389
Missense in Polyphen		41	35.415	1.1577		517
Synonymous	0.533	48	52.9	0.907	0.00000375	411
Loss of Function	1.31	4	7.98	0.501	3.90e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000363	0.000362
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000329	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000449	0.000448
Middle Eastern	0.000329	0.000272
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

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);PI3K-Akt Signaling Pathway;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i (Consensus)

Recessive Scores

• pRec: 0.0734

Intolerance Scores

• loftool: 0.311
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.0474
• hipred: N
• hipred_score: 0.318
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.685

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
• Cellular component: extracellular space;endoplasmic reticulum;vesicle
• Molecular function: growth hormone receptor binding;hormone activity;growth factor activity;metal ion binding