SOSTDC1

sclerostin domain containing 1, the group of DAN family

Basic information

Region (hg38): 7:16461480-16530580

Links

ENSG00000171243 ∙ NCBI:25928 ∙ OMIM:609675 ∙ HGNC:21748 ∙ Uniprot:Q6X4U4 ∙ 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 SOSTDC1 gene.

• not provided (5 variants)
• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOSTDC1 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					2	2
missense			4		2	6
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	5

Variants in SOSTDC1

This is a list of pathogenic ClinVar variants found in the SOSTDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-16462576-CT-C			Benign (Dec 31, 2019)
7-16462589-G-A		not specified	Uncertain significance (Aug 12, 2021)
7-16462639-T-C			Benign (Jan 08, 2018)
7-16462707-G-C			Benign (Jul 13, 2018)
7-16462765-T-C			Benign (Apr 01, 2024)
7-16462821-T-C			Benign (Apr 20, 2018)
7-16462835-T-C		not specified	Uncertain significance (Mar 06, 2023)
7-16462906-T-C		not specified	Uncertain significance (Dec 13, 2023)
7-16462930-G-C		not specified	Uncertain significance (Nov 12, 2021)
7-16465565-T-C		not specified	Uncertain significance (Apr 11, 2023)
7-16527002-T-G		not specified	Uncertain significance (Sep 16, 2022)
7-16527028-C-A		not specified	Uncertain significance (Nov 14, 2023)
7-16527040-C-T		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOSTDC1	protein_coding	protein_coding	ENST00000307068	2	69100

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.163	0.779	125739	0	6	125745	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.661	98	118	0.829	0.00000670	1351
Missense in Polyphen		41	64.328	0.63736		691
Synonymous	-0.781	48	41.6	1.15	0.00000201	393
Loss of Function	1.56	2	6.19	0.323	2.64e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the onset of endometrial receptivity for implantation/sensitization for the decidual cell reaction Enhances Wnt signaling and inhibits TGF-beta signaling (By similarity). Directly antagonizes activity of BMP2, BMP4, BMP6 and BMP7 in a dose-dependent manner. {ECO:0000250, ECO:0000269|PubMed:15020244}.
• Pathway: Vitamin D Receptor Pathway;EDA Signalling in Hair Follicle Development;BMP receptor signaling (Consensus)

Recessive Scores

• pRec: 0.158

Intolerance Scores

• loftool: 0.289
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.200
• hipred: Y
• hipred_score: 0.510
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.822

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sostdc1
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; skeleton phenotype

Gene ontology

• Biological process: pattern specification process;negative regulation of cell fate commitment;Wnt signaling pathway;negative regulation of Wnt signaling pathway;BMP signaling pathway;negative regulation of BMP signaling pathway;hair follicle morphogenesis;odontogenesis of dentin-containing tooth;negative regulation of myoblast differentiation;mammary gland bud morphogenesis;negative regulation of canonical Wnt signaling pathway;negative regulation of determination of dorsal identity
• Cellular component: extracellular space
• Molecular function: BMP binding;BMP receptor activity