Is DNHD1 p.Cys2065fs (c.6194del) pathogenic?

DNHD1 p.Cys2065fs (c.6194del) is classified Pathogenic in DNHD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-28). Absent from gnomAD.

How common is DNHD1 p.Cys2065fs (c.6194del) in the general population?

DNHD1 p.Cys2065fs (c.6194del) is absent from gnomAD (gnomAD).

DNHD1 p.Cys2065fs

c.6194del · rs1853238476 · VCV2147164

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

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 21 of 43
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.56	GERP 0.38

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: DNHD1
Protein: p.Cys2065fs
Coding: c.6194del
MANE Select: NM_144666
dbSNP: rs1853238476
Type: Deletion
Location: chr11:6547133 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)
Residue 2065: a UniProt-annotated variant site (in spgf65)

Full DNHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNHD1 p.Ala3219fs Likely pathogenic ★ same type
DNHD1 p.Ala4403fs Pathogenic ★ same type
DNHD1 p.Gln754fs Pathogenic ★ same type
DNHD1 p.Glu4334fs Likely pathogenic ★ same type
DNHD1 p.Gly768fs Pathogenic ★ same type
DNHD1 p.His1175fs Pathogenic ★ same type
DNHD1 p.Ile3016fs Pathogenic ★ same type
DNHD1 p.Leu1093fs Likely pathogenic ★ same type

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/dnhd1-p-cys2065fs (accessed [today's date]).

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