NHLH1

nescient helix-loop-helix 1, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 1:160367071-160372846

Previous symbols: [ "HEN1" ]

Links

ENSG00000171786 ∙ NCBI:4807 ∙ OMIM:162360 ∙ HGNC:7817 ∙ Uniprot:Q02575 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 2 of 2.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_005598.4	NP_005589.1	1	yes	-
ENST00000302101.6	ENSP00000302189.5	1	yes	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NHLH1 gene.

• not_specified (14 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NHLH1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_005598.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			15			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NHLH1	protein_coding	protein_coding	ENST00000302101	1	5782

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		120825	0	2	120827	0.00000828

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	71	100	0.708	0.00000804	824
Missense in Polyphen		16	29.58	0.54091		196
Synonymous	0.0858	46	46.7	0.984	0.00000353	311
Loss of Function	1.23	1	3.48	0.287	2.80e-7	31

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)	0.00000935	0.00000930
Middle Eastern	0.00	0.00
South Asian	0.0000336	0.0000329
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.

Recessive Scores

• pRec: 0.203

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;central nervous system development;cell differentiation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein dimerization activity