NHSL1

NHS like 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 6:138422042-138692571

Previous symbols: [ "C6orf63" ]

Links

ENSG00000135540 ∙ NCBI:57224 ∙ OMIM:620171 ∙ HGNC:21021 ∙ Uniprot:Q5SYE7 ∙ 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 NHSL1 gene.

• Inborn genetic diseases (67 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NHSL1 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	5	7
missense			63	5	1	69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	63	7	6

Variants in NHSL1

This is a list of pathogenic ClinVar variants found in the NHSL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-138424086-T-A		not specified	Uncertain significance (Sep 14, 2022)
6-138424160-C-T		not specified	Uncertain significance (Feb 05, 2024)
6-138424242-C-T		not specified	Uncertain significance (Jul 11, 2023)
6-138424274-G-A		not specified	Uncertain significance (Oct 13, 2023)
6-138424420-G-C			Benign (Aug 15, 2017)
6-138424487-T-C		not specified	Uncertain significance (Sep 27, 2021)
6-138424532-G-T		not specified	Uncertain significance (Jan 18, 2023)
6-138424535-G-A		not specified	Uncertain significance (Feb 06, 2023)
6-138424548-A-T		not specified	Uncertain significance (Dec 30, 2023)
6-138424596-T-G		not specified	Uncertain significance (May 24, 2023)
6-138424749-G-T		not specified	Uncertain significance (Aug 08, 2023)
6-138424760-T-C		not specified	Uncertain significance (Feb 10, 2022)
6-138424771-G-A			Benign (Dec 31, 2019)
6-138429750-C-T		not specified	Uncertain significance (Feb 07, 2023)
6-138430399-C-T		not specified	Uncertain significance (May 04, 2023)
6-138430443-G-A		not specified	Uncertain significance (Sep 20, 2023)
6-138430497-A-C		not specified	Uncertain significance (Dec 15, 2022)
6-138430545-G-C		not specified	Uncertain significance (Sep 26, 2022)
6-138430683-C-A		not specified	Uncertain significance (Dec 08, 2023)
6-138430693-C-G		not specified	Uncertain significance (Jan 02, 2024)
6-138430693-C-T		not specified	Uncertain significance (Dec 14, 2021)
6-138430699-G-T		not specified	Uncertain significance (Jan 04, 2024)
6-138430795-G-T		not specified	Uncertain significance (Oct 14, 2021)
6-138430854-G-C		not specified	Uncertain significance (Jan 08, 2024)
6-138430861-G-A		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NHSL1	protein_coding	protein_coding	ENST00000427025	7	270529

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.461	0.539	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	675	896	0.753	0.0000522	10392
Missense in Polyphen		250	366.1	0.68288		4243
Synonymous	3.10	301	378	0.797	0.0000245	3427
Loss of Function	4.85	10	45.2	0.221	0.00000260	548

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0881

Intolerance Scores

• rvis_EVS: 1.53
• rvis_percentile_EVS: 95.56

Haploinsufficiency Scores

• pHI: 0.169
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0173

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nhsl1
• Phenotype: hearing/vestibular/ear phenotype

Zebrafish Information Network

• Gene name: nhsl1b
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: cell differentiation