SDAD1

SDA1 domain containing 1, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 4:75940949-75990962

Links

ENSG00000198301 ∙ NCBI:55153 ∙ ∙ HGNC:25537 ∙ Uniprot:Q9NVU7 ∙ 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 SDAD1 gene.

• Inborn genetic diseases (22 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDAD1 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	2	3
missense			21	2		23
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	21	3	3

Variants in SDAD1

This is a list of pathogenic ClinVar variants found in the SDAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-75950758-T-C		not specified	Uncertain significance (Apr 13, 2022)
4-75950796-A-C		not specified	Uncertain significance (Jun 30, 2022)
4-75955992-A-T		not specified	Uncertain significance (Jun 12, 2023)
4-75956009-C-T		not specified	Uncertain significance (Jan 29, 2024)
4-75956030-A-G		not specified	Uncertain significance (Dec 26, 2023)
4-75956057-T-C		not specified	Uncertain significance (May 06, 2022)
4-75956072-G-A		not specified	Uncertain significance (Jan 31, 2024)
4-75957338-A-C		not specified	Uncertain significance (Jan 03, 2024)
4-75957378-G-A		not specified	Uncertain significance (Sep 16, 2021)
4-75957570-C-T		not specified	Uncertain significance (Mar 16, 2022)
4-75957574-G-C			Benign (Jan 05, 2018)
4-75957654-T-C		not specified	Likely benign (Sep 14, 2023)
4-75957683-A-G			Likely benign (Dec 01, 2022)
4-75957690-T-C		not specified	Uncertain significance (Mar 03, 2022)
4-75960123-T-G		not specified	Uncertain significance (Aug 12, 2021)
4-75960161-C-G		not specified	Uncertain significance (Oct 12, 2022)
4-75961075-G-T		not specified	Uncertain significance (Feb 15, 2023)
4-75961261-G-C		not specified	Uncertain significance (Oct 25, 2023)
4-75961298-T-C		not specified	Uncertain significance (Jan 03, 2024)
4-75964187-C-T		not specified	Uncertain significance (Feb 28, 2024)
4-75967321-T-C		not specified	Uncertain significance (Dec 03, 2021)
4-75967344-G-T			Benign (May 21, 2018)
4-75969319-A-C		not specified	Uncertain significance (Jun 06, 2022)
4-75970362-T-C		not specified	Uncertain significance (Dec 19, 2023)
4-75971416-T-C		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDAD1	protein_coding	protein_coding	ENST00000356260	22	50013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.83e-20	0.0798	125670	0	78	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0327	362	360	1.00	0.0000181	4610
Missense in Polyphen		36	53.766	0.66956		801
Synonymous	0.183	122	125	0.979	0.00000618	1185
Loss of Function	1.31	36	45.5	0.791	0.00000259	521

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000832	0.000826
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000330	0.000326
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000240	0.000237
Middle Eastern	0.000330	0.000326
South Asian	0.000741	0.000719
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for 60S pre-ribosomal subunits export to the cytoplasm. {ECO:0000250}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.942
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.5

Haploinsufficiency Scores

• pHI: 0.100
• hipred: Y
• hipred_score: 0.637
• ghis: 0.575

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.917

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sdad1

Zebrafish Information Network

• Gene name: sdad1
• Affected structure: mandibular arch skeleton
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: ribosomal large subunit export from nucleus;actin cytoskeleton organization;ribosomal large subunit biogenesis
• Cellular component: nucleus;nucleolus
• Molecular function: molecular_function