DCHS2

dachsous cadherin-related 2, the group of Cadherin related

Basic information

Region (hg38): 4:154231741-154491799

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.

• Inborn genetic diseases (40 variants)
• not provided (10 variants)
• Multiple congenital anomalies (1 variants)
• DCHS2-related condition (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.

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				3		3
missense			32	12		44
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			3			3
Total	0	0	37	15	0

Variants in DCHS2

This is a list of pathogenic ClinVar variants found in the DCHS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-154234645-G-A		DCHS2-related disorder	Likely benign (Apr 06, 2022)
4-154234762-G-A		DCHS2-related disorder	Benign (Jun 04, 2019)
4-154235055-G-A		DCHS2-related disorder	Benign (Oct 17, 2019)
4-154235095-G-A		DCHS2-related disorder	Benign (Sep 19, 2019)
4-154235247-G-A		DCHS2-related disorder	Benign (Jun 26, 2019)
4-154235260-G-A		DCHS2-related disorder	Benign (Sep 19, 2019)
4-154235390-G-A		DCHS2-related disorder	Benign (Aug 08, 2019)
4-154235446-G-A		DCHS2-related disorder	Likely benign (Apr 18, 2022)
4-154235522-G-A		DCHS2-related disorder	Likely benign (Nov 26, 2019)
4-154235598-T-A		DCHS2-related disorder	Benign (Mar 14, 2019)
4-154235723-T-G		DCHS2-related disorder	Benign (Mar 03, 2020)
4-154235863-T-C		DCHS2-related disorder	Benign (May 28, 2019)
4-154236008-G-T		DCHS2-related disorder	Benign (Feb 20, 2019)
4-154236252-C-T		DCHS2-related disorder	Benign (Jun 07, 2019)
4-154236379-C-T		DCHS2-related disorder	Benign (Mar 14, 2019)
4-154236578-G-A		DCHS2-related disorder	Benign (Sep 19, 2019)
4-154236719-A-G		DCHS2-related disorder	Benign (Feb 27, 2019)
4-154236801-A-G		DCHS2-related disorder	Benign (Sep 10, 2019)
4-154236809-C-T		DCHS2-related disorder	Benign (Mar 14, 2019)
4-154236938-A-C		DCHS2-related disorder	Benign (Feb 27, 2019)
4-154237132-A-C		DCHS2-related disorder	Likely benign (Sep 12, 2022)
4-154239272-A-AC		DCHS2-related disorder	Benign (Feb 27, 2019)
4-154239277-A-G		DCHS2-related disorder	Benign (Feb 27, 2019)
4-154240735-A-G		DCHS2-related disorder	Benign (Mar 15, 2019)
4-154242632-TCA-T		DCHS2-related disorder	Benign (Dec 24, 2019)

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

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

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