CSHL1

chorionic somatomammotropin hormone like 1, the group of Growth hormone family

Basic information

Region (hg38): 17:63909597-63911341

Previous symbols: [ "CSHP1" ]

Links

ENSG00000204414 ∙ NCBI:1444 ∙ OMIM:603515 ∙ HGNC:2442 ∙ Uniprot:Q14406 ∙ 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 CSHL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSHL1 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			13	3	2	18
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	14	4	3

Variants in CSHL1

This is a list of pathogenic ClinVar variants found in the CSHL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63909806-C-T		not specified	Uncertain significance (Oct 25, 2023)
17-63909840-G-C		not specified	Uncertain significance (Dec 22, 2023)
17-63909886-A-C		not specified	Likely benign (Sep 17, 2021)
17-63909889-T-C		not specified	Uncertain significance (Sep 17, 2021)
17-63910212-C-A		not specified	Uncertain significance (Jan 16, 2024)
17-63910230-C-G		not specified	Uncertain significance (Mar 23, 2023)
17-63910248-T-C			Benign (Jun 18, 2018)
17-63910252-G-C			Benign (Jun 18, 2018)
17-63910253-G-A			Benign (Jun 18, 2018)
17-63910283-C-T		not specified	Uncertain significance (Jun 17, 2024)
17-63910284-G-A		not specified	Likely benign (Apr 07, 2022)
17-63910419-C-T			Likely benign (Dec 01, 2022)
17-63910424-T-A		not specified	Uncertain significance (Sep 06, 2022)
17-63910433-G-A		not specified	Uncertain significance (Apr 20, 2024)
17-63910441-C-G		not specified	Uncertain significance (Jan 09, 2024)
17-63910486-C-G		not specified	Uncertain significance (Oct 25, 2022)
17-63910490-G-A		not specified	Uncertain significance (May 02, 2024)
17-63910511-T-G		not specified	Uncertain significance (Jan 24, 2023)
17-63910533-C-T		not specified	Uncertain significance (Apr 13, 2023)
17-63910799-C-T		not specified	Uncertain significance (May 26, 2022)
17-63910802-G-C		not specified	Uncertain significance (Apr 14, 2022)
17-63910858-G-A		not specified	Uncertain significance (Feb 17, 2022)
17-63910882-A-G		not specified	Uncertain significance (Jun 24, 2022)
17-63910918-C-T		not specified	Likely benign (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSHL1	protein_coding	protein_coding	ENST00000309894	5	9242

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.08e-12	0.00605	124741	21	986	125748	0.00401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.74	181	126	1.43	0.00000798	1454
Missense in Polyphen		85	60.539	1.404		772
Synonymous	-2.53	79	55.1	1.43	0.00000359	427
Loss of Function	-1.30	15	10.5	1.43	5.56e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0479	0.0476
Ashkenazi Jewish	0.00248	0.00248
East Asian	0.00332	0.00332
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000687	0.000677
Middle Eastern	0.00332	0.00332
South Asian	0.000555	0.000555
Other	0.00375	0.00375

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a novel gestational hormone required to compensate for absence of other members of the GH/CS cluster during gestation. {ECO:0000269|PubMed:8083227}.

Recessive Scores

• pRec: 0.0881

Intolerance Scores

• loftool: 0.123
• rvis_EVS: 1.2
• rvis_percentile_EVS: 92.95

Haploinsufficiency Scores

• pHI: 0.0432
• hipred: N
• hipred_score: 0.166

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.506

Gene Damage Prediction

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

Gene ontology

• Biological process: 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: cellular_component;extracellular space
• Molecular function: growth hormone receptor binding;hormone activity;growth factor activity;metal ion binding