Is DHX37 p.Arg792Gln (c.2375G>A) pathogenic?

DHX37 p.Arg792Gln (c.2375G>A) is classified Conflicting classifications of pathogenicity in DHX37 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-01-21). AlphaMissense: likely benign (0.0674); Ultra-rare (popmax 0.0836%, sas); Associated with Inborn genetic diseases.

What condition is associated with DHX37 p.Arg792Gln (c.2375G>A)?

DHX37 p.Arg792Gln (c.2375G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DHX37 p.Arg792Gln (c.2375G>A) in the general population?

DHX37 p.Arg792Gln (c.2375G>A) is ultra-rare (popmax 0.0836%, sas) (gnomAD).

What do computational predictors say about DHX37 p.Arg792Gln (c.2375G>A)?

AlphaMissense predicts likely benign (score 0.0674) — an in-silico prediction, not a clinical call.

DHX37 p.Arg792Gln

c.2375G>A · rs747470305 · VCV2342808

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0674 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0836%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0674	likely benign
REVEL	0.096	moderately benign-leaning
SaProt	LLR -5.62	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.1	GERP -1.4
Regional constraint	o/e 0.86	unconstrained · MANE · 13 kb · p 0.00031 · regional, not allelic
Overall
CADD	12.14	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 0.0836% South Asian · 76/90,952 alleles

Filtering AF 0.0684% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0629%

Overall 0.00801% 129/1,610,720 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0836%	1,197
Middle Eastern	0.0165%	6,070
European (non-Finnish)	0.00391%	25,600
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,568
Admixed American	0.00334%	29,962
Remaining individualsnot grpmax-eligible	0.00321%	31,135
East Asian	0.00223%	44,752

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: DHX37
Protein: p.Arg792Gln
Coding: c.2375G>A
MANE Select: NM_032656
dbSNP: rs747470305
Type: single nucleotide variant
Location: chr12:124956769 (GRCh38)
Gene constraint: LOEUF 0.518 · pLI 0.20 (gnomAD)
Structure: AlphaFold pLDDT 76.27 · 1 PDB

Full DHX37 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DHX37 p.Arg792Ter Likely pathogenic ★ same residue
DHX37 p.Ala1142Gly Uncertain significance ★★ ⚠ same condition
DHX37 p.Ala469Ser Uncertain significance ★★ ⚠ same condition
DHX37 p.Ala687Val Uncertain significance ★★ ⚠ same condition
DHX37 p.Ala743Thr Uncertain significance ★★ ⚠ same condition
DHX37 p.Arg1029Pro Uncertain significance ★★ ⚠ same condition
DHX37 p.Arg1042His Uncertain significance ★★ ⚠ same condition
DHX37 p.Arg1060His 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/dhx37-p-arg792gln (accessed [today's date]).

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