LY6G6F-LY6G6D

LY6G6F-LY6G6D readthrough

Basic information

Region (hg38): 6:31706903-31717918

Links

ENSG00000250641 ∙ NCBI:110599563 ∙ ∙ HGNC:38821 ∙ ∙ ∙ 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 LY6G6F-LY6G6D gene.

• Inborn genetic diseases (18 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LY6G6F-LY6G6D 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			14	1	1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	17	1	1

Variants in LY6G6F-LY6G6D

This is a list of pathogenic ClinVar variants found in the LY6G6F-LY6G6D region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31707506-C-A			Benign (Feb 20, 2018)
6-31707517-C-T		not specified	Uncertain significance (Jan 19, 2022)
6-31707523-A-G		not specified	Uncertain significance (Mar 12, 2024)
6-31707538-G-A		not specified	Uncertain significance (Jul 05, 2023)
6-31707631-A-C		not specified	Uncertain significance (Feb 07, 2023)
6-31707680-G-C		not specified	Uncertain significance (Apr 25, 2023)
6-31707718-T-G		not specified	Uncertain significance (Jan 10, 2023)
6-31707886-C-T		not specified	Uncertain significance (May 17, 2023)
6-31707904-C-A		not specified	Uncertain significance (Sep 14, 2023)
6-31707985-T-G		not specified	Uncertain significance (Feb 15, 2023)
6-31707993-C-T		not specified	Uncertain significance (Nov 23, 2021)
6-31708003-C-T		not specified	Uncertain significance (Oct 13, 2021)
6-31710088-C-G		not specified	Uncertain significance (Mar 04, 2024)
6-31710166-G-T		not specified	Uncertain significance (Oct 05, 2023)
6-31710358-C-T		not specified	Uncertain significance (Dec 11, 2023)
6-31710397-A-G		not specified	Uncertain significance (Apr 17, 2023)
6-31710399-A-T		not specified	Uncertain significance (Mar 03, 2022)
6-31710411-C-T		not specified	Uncertain significance (Oct 29, 2021)
6-31715520-A-G		not specified	Uncertain significance (Jan 10, 2023)
6-31715561-G-A		not specified	Uncertain significance (Sep 30, 2021)
6-31715579-G-A		not specified	Uncertain significance (Apr 17, 2023)
6-31715583-G-A		not specified	Likely benign (Sep 16, 2021)
6-31717619-G-A		not specified	Uncertain significance (Jul 08, 2022)
6-31717778-C-A		not specified	Uncertain significance (Dec 18, 2023)
6-31717799-G-A		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LY6G6F-LY6G6D	protein_coding	protein_coding	ENST00000503322	6	11015

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.23e-7	0.587	125633	0	114	125747	0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.651	197	224	0.878	0.0000123	2437
Missense in Polyphen		44	55.984	0.78594		680
Synonymous	1.32	77	93.2	0.826	0.00000543	821
Loss of Function	1.05	13	17.8	0.732	0.00000103	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000978	0.000973
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000524	0.000519
Middle Eastern	0.00	0.00
South Asian	0.000622	0.000621
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP