Is ZFPM2 p.Pro810= (c.2430A>T) pathogenic?

ZFPM2 p.Pro810= (c.2430A>T) is classified Benign/Likely benign in ZFPM2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-22). Rare (popmax 0.198%, mid); Associated with 46,XY sex reversal 9.

What condition is associated with ZFPM2 p.Pro810= (c.2430A>T)?

ZFPM2 p.Pro810= (c.2430A>T) is associated with 46,XY sex reversal 9 (ClinVar).

How common is ZFPM2 p.Pro810= (c.2430A>T) in the general population?

ZFPM2 p.Pro810= (c.2430A>T) is rare (popmax 0.198%, mid) (gnomAD).

ZFPM2 p.Pro810=

c.2430A>T · rs200002039 · VCV1167133

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.198%, mid)

Conditions

46,XY sex reversal 9

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -13	GERP -3.7
Overall
CADD	0.029	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.198% Middle Eastern · 12/6,060 alleles

Filtering AF 0.114% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0895%

Overall 0.0102% 164/1,612,262 alleles · rare exomes 141/1,459,970 · genomes 23/152,292 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.298%	335
Middle Easterngrpmax	0.198%	505
Remaining individualsnot grpmax-eligible	0.0336%	2,973
South Asian	0.0121%	8,248
European (non-Finnish)	0.00263%	38,037
African / African-American	0.00133%	75,032

Ashkenazi Jewish 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: ZFPM2
Protein: p.Pro810=
Coding: c.2430A>T
MANE Select: NM_012082
dbSNP: rs200002039
Type: single nucleotide variant
Location: chr8:105802512 (GRCh38)

Full ZFPM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

46,XY sex reversal 9 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/zfpm2-p-pro810 (accessed [today's date]).

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