SAYSD1

SAYSVFN motif domain containing 1

Basic information

Region (hg38): 6:39104063-39115193

Previous symbols: [ "C6orf64" ]

Links

ENSG00000112167 ∙ NCBI:55776 ∙ ∙ HGNC:21025 ∙ Uniprot:Q9NPB0 ∙ 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 SAYSD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAYSD1 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						0
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in SAYSD1

This is a list of pathogenic ClinVar variants found in the SAYSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-39105436-C-T		not specified	Uncertain significance (May 08, 2023)
6-39105456-C-A		not specified	Uncertain significance (Dec 14, 2022)
6-39105466-C-T		not specified	Uncertain significance (Oct 28, 2024)
6-39105514-G-A		not specified	Uncertain significance (Apr 04, 2024)
6-39105532-G-A		not specified	Uncertain significance (Jul 14, 2024)
6-39105575-C-T		not specified	Uncertain significance (Jul 19, 2024)
6-39105595-A-G		not specified	Uncertain significance (May 04, 2023)
6-39105686-T-C		not specified	Uncertain significance (Dec 28, 2023)
6-39105697-G-C		not specified	Uncertain significance (Aug 20, 2024)
6-39105733-T-C		not specified	Uncertain significance (Aug 26, 2024)
6-39105776-C-T		not specified	Uncertain significance (Oct 06, 2021)
6-39114884-T-A		not specified	Uncertain significance (Jan 23, 2024)
6-39114897-G-C		not specified	Uncertain significance (Feb 28, 2024)
6-39114915-C-T		not specified	Uncertain significance (Jan 27, 2025)
6-39114919-C-A		not specified	Uncertain significance (Mar 18, 2024)
6-39114941-C-T		not specified	Uncertain significance (May 17, 2023)
6-39114965-T-G		not specified	Uncertain significance (Jul 08, 2022)
6-39115005-G-C		not specified	Uncertain significance (Apr 01, 2024)
6-39115028-G-A		not specified	Uncertain significance (Jan 17, 2024)
6-39115029-G-T		not specified	Uncertain significance (Sep 01, 2021)
6-39115046-G-T		not specified	Uncertain significance (Oct 26, 2022)
6-39115079-C-T		not specified	Uncertain significance (Jun 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAYSD1	protein_coding	protein_coding	ENST00000229903	2	11126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000374	0.390	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.530	118	103	1.15	0.00000533	1142
Missense in Polyphen		39	34.847	1.1192		415
Synonymous	0.297	46	48.6	0.946	0.00000270	409
Loss of Function	0.226	7	7.67	0.912	4.30e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000403	0.000398
Ashkenazi Jewish	0.000595	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000459	0.000431
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000329	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.89

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.170
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Saysd1

Gene ontology

• Cellular component: integral component of membrane;cytoplasmic vesicle membrane;intracellular membrane-bounded organelle