Is DNHD1 p.Gln39Arg (c.116A>G) pathogenic?

DNHD1 p.Gln39Arg (c.116A>G) is classified Likely benign in DNHD1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-09-01). AlphaMissense: likely benign (0.0781); Rare (popmax 0.756%, sas).

How common is DNHD1 p.Gln39Arg (c.116A>G) in the general population?

DNHD1 p.Gln39Arg (c.116A>G) is rare (popmax 0.756%, sas) (gnomAD).

What do computational predictors say about DNHD1 p.Gln39Arg (c.116A>G)?

AlphaMissense predicts likely benign (score 0.0781) — an in-silico prediction, not a clinical call.

DNHD1 p.Gln39Arg

c.116A>G · rs140872512 · VCV788110

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.0781 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.756%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0781	likely benign
REVEL	0.043	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.27	GERP 0.71
Regional constraint	o/e 0.90	unconstrained · MANE · 66 kb · p 5.3e-11 · regional, not allelic
Overall
CADD	6.792	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.756% South Asian · 689/91,092 alleles

Filtering AF 0.71% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.691%

Overall 0.134% 2,170/1,614,246 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.756%	132
Middle Eastern	0.363%	276
Admixed American	0.265%	378
Remaining individualsnot grpmax-eligible	0.194%	517
European (non-Finnish)	0.0947%	1,055
Ashkenazi Jewishnot grpmax-eligible	0.0946%	1,057
Finnishnot grpmax-eligible	0.0265%	3,768
African / African-American	0.0213%	4,691

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DNHD1
Protein: p.Gln39Arg
Coding: c.116A>G
MANE Select: NM_144666
dbSNP: rs140872512
Type: single nucleotide variant
Location: chr11:6498331 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)

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

Similar variants

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DNHD1 p.Arg1582Trp Uncertain significance ★★ same type
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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-gln39arg (accessed [today's date]).

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