Is DHH p.Pro9Ala (c.25C>G) pathogenic?

DHH p.Pro9Ala (c.25C>G) is classified Benign/Likely benign in DHH (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-23). AlphaMissense: likely benign (0.0557); Very rare (popmax 0.00866%, nfe); Associated with 46,XY sex reversal 7.

What condition is associated with DHH p.Pro9Ala (c.25C>G)?

DHH p.Pro9Ala (c.25C>G) is associated with 46,XY sex reversal 7 (ClinVar).

How common is DHH p.Pro9Ala (c.25C>G) in the general population?

DHH p.Pro9Ala (c.25C>G) is very rare (popmax 0.00866%, nfe) (gnomAD).

What do computational predictors say about DHH p.Pro9Ala (c.25C>G)?

AlphaMissense predicts likely benign (score 0.0557) — an in-silico prediction, not a clinical call.

DHH p.Pro9Ala

c.25C>G · rs200685404 · VCV2727400

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0557 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00866%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

46,XY sex reversal 7

Computational evidence

Protein change
AlphaMissense	0.0557	likely benign
REVEL	0.407	indeterminate
SaProt	LLR -4.24	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.6	GERP 1.1, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 4,650 bp · p 8.5e-08 · regional, not allelic
Overall
CADD	17.2	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 0.00866% European (non-Finnish) · 100/1,154,920 alleles

Filtering AF 0.00723% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00674%

Overall 0.0613% 959/1,564,508 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	1.38%	72
Remaining individualsnot grpmax-eligible	0.0643%	1,555
European (non-Finnish)grpmax	0.00866%	11,549
East Asian	0.0024%	41,634

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DHH
Protein: p.Pro9Ala
Coding: c.25C>G
MANE Select: NM_021044
dbSNP: rs200685404
Type: single nucleotide variant
Location: chr12:49094488 (GRCh38)
Gene constraint: LOEUF 0.999 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.87 · 5 PDB

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

Disease context

46,XY sex reversal 7 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DHH c.*401G>T Uncertain significance ★★ same condition
DHH p.Ala287Glu Uncertain significance ★★ ⚠ same condition
DHH p.Arg102His Uncertain significance ★★ ⚠ same condition
DHH p.Arg309Leu Uncertain significance ★★ ⚠ same condition
DHH p.Arg318Pro Uncertain significance ★★ ⚠ same condition
DHH p.Ser210Arg Uncertain significance ★★ ⚠ same condition
DHH c.304-15T>C Likely benign ★★ same condition
DHH c.-255T>C Benign ★★ 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/dhh-p-pro9ala (accessed [today's date]).

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