Is NHS p.Arg17fs (c.50_53del) pathogenic?

NHS p.Arg17fs (c.5053del) is classified Pathogenic in NHS (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-25). No gnomAD frequency available for this variant; Associated with Nance-Horan syndrome.

What condition is associated with NHS p.Arg17fs (c.50_53del)?

NHS p.Arg17fs (c.50_53del) is associated with Nance-Horan syndrome (ClinVar).

How common is NHS p.Arg17fs (c.50_53del) in the general population?

NHS p.Arg17fs (c.50_53del) is no gnomAD frequency available for this variant (gnomAD).

NHS p.Arg17fs

c.50_53del · rs2146834311 · VCV1446464

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Nance-Horan syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 1 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.6	GERP -0.11, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: NHS
Protein: p.Arg17fs
Coding: c.50_53del
MANE Select: NM_001291867
dbSNP: rs2146834311
Type: Deletion
Location: chrX:17375807 (GRCh38)
Structure: AlphaFold pLDDT 43.65
Residue 17: the 'wave homology domain (whd)' region; the 'disordered' region

Full NHS gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Nance-Horan syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NHS p.Arg17Gln Uncertain significance ★ same residue
NHS p.Ala1306fs Pathogenic/Likely pathogenic ★★ same condition
NHS p.Arg17Trp Uncertain significance ★★ same residue
NHS p.Ser110_Ala116del Uncertain significance ★★ same condition
NHS p.Pro104_Ala115del Benign ★★ same condition
NHS p.Ala117fs Likely pathogenic ★ same condition
NHS p.Arg468fs Likely pathogenic ★ same condition
NHS p.Asp488fs Pathogenic ★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/nhs-p-arg17fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown