NHSL2

NHS like 2

Basic information

Region (hg38): X:71910845-72161750

Links

ENSG00000204131 ∙ NCBI:340527 ∙ OMIM:301093 ∙ HGNC:33737 ∙ Uniprot:Q5HYW2 ∙ 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 NHSL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NHSL2 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				4		4
missense			64	3		67
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			30	6	1	37
Total	0	0	94	13	1

Variants in NHSL2

This is a list of pathogenic ClinVar variants found in the NHSL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-71911104-G-T		not specified	Uncertain significance (Mar 31, 2024)
X-71911121-C-T		not specified	Uncertain significance (Feb 14, 2023)
X-71911143-C-G		not specified	Uncertain significance (Jun 16, 2024)
X-71911185-C-G		not specified	Uncertain significance (Dec 13, 2022)
X-71911278-G-A		not specified	Uncertain significance (Feb 14, 2023)
X-71911332-G-A		not specified	Uncertain significance (Jan 26, 2023)
X-72129877-G-A		not specified	Uncertain significance (Apr 06, 2024)
X-72129887-G-A		not specified	Conflicting classifications of pathogenicity (Dec 06, 2023)
X-72129904-C-T		not specified	Uncertain significance (Dec 26, 2023)
X-72129941-G-A			Likely benign (Mar 01, 2023)
X-72129943-C-T		not specified	Uncertain significance (Jan 29, 2024)
X-72129958-G-C		not specified	Uncertain significance (Nov 08, 2022)
X-72130009-C-T		not specified	Uncertain significance (Aug 02, 2022)
X-72130073-C-G		not specified	Uncertain significance (Oct 13, 2023)
X-72130112-C-G		not specified	Uncertain significance (Oct 04, 2022)
X-72130112-C-T		not specified	Likely benign (Jun 01, 2023)
X-72130205-C-T		not specified	Uncertain significance (May 23, 2024)
X-72130277-C-G		not specified	Uncertain significance (Aug 26, 2022)
X-72130282-C-T		not specified	Likely benign (Jan 04, 2024)
X-72130283-T-G			Benign (Sep 25, 2021)
X-72130288-C-A		not specified	Uncertain significance (Aug 02, 2023)
X-72130373-T-C		not specified	Likely benign (Jun 17, 2024)
X-72130403-C-T		not specified	Uncertain significance (Jan 23, 2024)
X-72130447-C-G		not specified	Uncertain significance (Sep 20, 2023)
X-72130490-C-G		not specified	Uncertain significance (May 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NHSL2	protein_coding	protein_coding	ENST00000540800	8	232487

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.117	0.883	125472	1	211	125684	0.000844

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.737	393	436	0.901	0.0000340	7861
Missense in Polyphen		104	134.36	0.77407		2458
Synonymous	0.724	167	179	0.931	0.0000143	2635
Loss of Function	3.23	6	22.6	0.266	0.00000162	457

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00335	0.00261
Ashkenazi Jewish	0.000678	0.000497
East Asian	0.00110	0.000816
Finnish	0.00224	0.00162
European (Non-Finnish)	0.00128	0.000898
Middle Eastern	0.00110	0.000816
South Asian	0.000105	0.0000653
Other	0.00204	0.00147

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.167
• hipred: N
• hipred_score: 0.226
• ghis: 0.475

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nhsl2

Gene ontology

• Biological process: cell differentiation