DCHS2

dachsous cadherin-related 2, the group of Cadherin related

Basic information

Region (hg38): 4:154231742-154491799

Previous symbols: [ "CDH27", "PCDH23" ]

Links

ENSG00000197410

∙ NCBI:54798 ∙ OMIM:612486 ∙ HGNC:23111 ∙ Uniprot:Q6V1P9 ∙ 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 DCHS2 gene.

not_specified (109 variants)
DCHS2-related_disorder (74 variants)
not_provided (13 variants)
Prostate_cancer (1 variants)
Multiple_congenital_anomalies (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCHS2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001358235.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar	17 clinvar	25
missense			95 clinvar	22 clinvar	27 clinvar	144
nonsense				1 clinvar		1
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	96	31	45

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCHS2	protein_coding	protein_coding	ENST00000357232	25	259532

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.42e-47	0.0000406	122574	15	3159	125748	0.0127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.497	1563	1.51e+3	1.04	0.0000747	19159
Missense in Polyphen		475	470.22	1.0102		6412
Synonymous	-1.05	617	585	1.06	0.0000312	5796
Loss of Function	1.34	79	92.9	0.850	0.00000437	1287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0148	0.0148
Ashkenazi Jewish	0.00697	0.00687
East Asian	0.00474	0.00474
Finnish	0.00704	0.00705
European (Non-Finnish)	0.0191	0.0190
Middle Eastern	0.00474	0.00474
South Asian	0.00853	0.00833
Other	0.0120	0.0120

dbNSFP

Source: dbNSFP

Function: FUNCTION: Calcium-dependent cell-adhesion protein. {ECO:0000250}.;
Pathway: Hippo signaling pathway - multiple species - Homo sapiens (human) (Consensus)

Intolerance Scores

loftool: 0.986
rvis_EVS: 7.75
rvis_percentile_EVS: 99.94

Haploinsufficiency Scores

pHI: 0.0631
hipred: N
hipred_score: 0.144
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0619

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Dchs2
Phenotype

Zebrafish Information Network

Gene name: dchs2
Affected structure: palatoquadrate cartilage
Phenotype tag: abnormal
Phenotype quality: disrupted

Gene ontology

Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;biological_process
Cellular component: cellular_component;plasma membrane;integral component of membrane
Molecular function: molecular_function;calcium ion binding