Is RECQL4 p.Pro820= (c.2460C>T) pathogenic?

RECQL4 p.Pro820= (c.2460C>T) is classified Benign/Likely benign in RECQL4 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-06-01). Rare (popmax 0.194%, nfe); Associated with Inborn genetic diseases.

What condition is associated with RECQL4 p.Pro820= (c.2460C>T)?

RECQL4 p.Pro820= (c.2460C>T) is associated with Inborn genetic diseases, Baller-Gerold syndrome, hereditary neoplastic syndrome (ClinVar).

How common is RECQL4 p.Pro820= (c.2460C>T) in the general population?

RECQL4 p.Pro820= (c.2460C>T) is rare (popmax 0.194%, nfe) (gnomAD).

RECQL4 p.Pro820=

c.2460C>T · rs202078917 · VCV239728

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

gnomAD v4.1

Rare

rare (popmax 0.194%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.1	GERP -3.9, phastCons 0.13
Overall
CADD	1.16	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.194% European (non-Finnish) · 2,264/1,166,882 alleles

Filtering AF 0.187% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.185%

Overall 0.156% 2,457/1,579,106 alleles · rare exomes 2,318/1,426,804 · genomes 139/152,302 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.194%	515
Remaining individualsnot grpmax-eligible	0.163%	612
Admixed American	0.083%	1,204
Middle Eastern	0.0356%	2,808
African / African-American	0.0335%	2,987
Ashkenazi Jewishnot grpmax-eligible	0.0312%	3,206
Finnishnot grpmax-eligible	0.0124%	8,064
South Asian	0.00224%	44,644

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: RECQL4
Protein: p.Pro820=
Coding: c.2460C>T
MANE Select: NM_004260
dbSNP: rs202078917
Type: single nucleotide variant
Location: chr8:144513221 (GRCh38)
Gene constraint: LOEUF 1.519 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32 · 2 PDB
Residue 820: the helicase c-terminal domain; a UniProt-annotated variant site (in rts2)

Full RECQL4 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

Also linked: Baller-Gerold syndrome hereditary neoplastic syndrome

Similar variants

RECQL4 p.Pro820Ala Uncertain significance ★ ⚠ same residue
RECQL4 p.Pro820Arg Uncertain significance ★ ⚠ same residue
RECQL4 p.Pro820Leu Uncertain significance ★ ⚠ same residue
RECQL4 p.Pro820_Gln821del Uncertain significance ★ same residue
RECQL4 c.1132-1G>A Likely pathogenic ★★ same condition
RECQL4 c.1259-1G>A Pathogenic/Likely pathogenic ★★ same condition
RECQL4 c.1391-1G>A Pathogenic ★★ same condition
RECQL4 c.1704+1G>A Pathogenic/Likely pathogenic ★★ 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/recql4-p-pro820 (accessed [today's date]).

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