Is OGDHL p.Pro37= (c.111G>A) pathogenic?

OGDHL p.Pro37= (c.111G>A) is classified Likely benign in OGDHL (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-10). Ultra-rare (popmax 0.0585%, nfe); Associated with OGDHL-related disorder.

What condition is associated with OGDHL p.Pro37= (c.111G>A)?

OGDHL p.Pro37= (c.111G>A) is associated with OGDHL-related disorder (ClinVar).

How common is OGDHL p.Pro37= (c.111G>A) in the general population?

OGDHL p.Pro37= (c.111G>A) is ultra-rare (popmax 0.0585%, nfe) (gnomAD).

OGDHL p.Pro37=

c.111G>A · rs138949514 · VCV3050206

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0585%, nfe)

Conditions

OGDHL-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -6	GERP -3.8
Overall
CADD	1.36	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0585% European (non-Finnish) · 690/1,180,044 alleles

Filtering AF 0.0548% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0534%

Overall 0.0462% 746/1,613,754 alleles · ultra-rare exomes 705/1,461,600 · genomes 41/152,154 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0585%	1,710
Remaining individualsnot grpmax-eligible	0.0512%	1,952
Finnishnot grpmax-eligible	0.0157%	6,377
Admixed American	0.0117%	8,573
African / African-American	0.00668%	14,978
East Asian	0.00446%	22,441

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: OGDHL
Protein: p.Pro37=
Coding: c.111G>A
MANE Select: NM_018245
dbSNP: rs138949514
Type: single nucleotide variant
Location: chr10:49758482 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.44

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

Disease context

OGDHL-related disorder

Similar variants

OGDHL p.Pro37Leu Uncertain significance ★ ⚠ same residue
OGDHL p.Arg965His Uncertain significance ★ ⚠ same condition
OGDHL c.1297-4G>A Likely benign same condition
OGDHL p.Ala630Val Benign same condition
OGDHL p.Ala876= Benign same condition
OGDHL p.Asp398= Likely benign same condition
OGDHL p.Leu164= Likely benign same condition
OGDHL p.Leu18= 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/ogdhl-p-pro37 (accessed [today's date]).

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