Is NHS p.Asp79= (c.237C>T) pathogenic?

NHS p.Asp79= (c.237C>T) is classified Likely benign in NHS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-29). No allele count reported in gnomAD v4.1 (AN 1,079,432); Associated with Nance-Horan syndrome.

What condition is associated with NHS p.Asp79= (c.237C>T)?

NHS p.Asp79= (c.237C>T) is associated with Nance-Horan syndrome (ClinVar).

How common is NHS p.Asp79= (c.237C>T) in the general population?

NHS p.Asp79= (c.237C>T) is no allele count reported in gnomAD v4.1 (AN 1,079,432) (gnomAD).

NHS p.Asp79=

c.237C>T · VCV3694811

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,079,432)

Conditions

Nance-Horan syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.35	GERP -1.8, phastCons 0.34
Overall
CADD	4.264	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,079,432). 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.Asp79=
Coding: c.237C>T
MANE Select: NM_001291867
Type: single nucleotide variant
Location: chrX:17375994 (GRCh38)
Structure: AlphaFold pLDDT 43.65
Residue 79: 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.Asp79fs Pathogenic ★ same residue
NHS p.Arg248Ter Pathogenic ★★ same condition
NHS p.Arg394Ter Pathogenic ★★ same condition
NHS p.Arg900Ter Pathogenic ★★ same condition
NHS p.Gln411Ter Pathogenic ★★ same condition
NHS p.Gln80Ter Pathogenic/Likely pathogenic ★★ same condition
NHS p.Ala564Val Uncertain significance ★★ same condition
NHS p.Ala745Val Uncertain significance ★★ 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-asp79 (accessed [today's date]).

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