Is SLX4 p.Ser30= (c.90C>T) pathogenic?

SLX4 p.Ser30= (c.90C>T) is classified Benign/Likely benign in SLX4 (ClinVar, Multiple submitters, 12 submitters; last evaluated 2026-05-01). Rare (popmax 0.979%, nfe); Associated with Fanconi anemia complementation group P.

What condition is associated with SLX4 p.Ser30= (c.90C>T)?

SLX4 p.Ser30= (c.90C>T) is associated with Fanconi anemia complementation group P, Fanconi anemia (ClinVar).

How common is SLX4 p.Ser30= (c.90C>T) in the general population?

SLX4 p.Ser30= (c.90C>T) is rare (popmax 0.979%, nfe) (gnomAD).

SLX4 p.Ser30=

c.90C>T · rs118089506 · VCV241701

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 12 submitters

gnomAD v4.1

Rare

rare (popmax 0.979%, nfe)

Conditions

Fanconi anemia complementation group P

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 1.2	GERP -2.5, phastCons 0.55
Overall
CADD	6.809	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.979% European (non-Finnish) · 11,550/1,180,038 alleles

Filtering AF 0.964% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.958%

Overall 0.833% 13,438/1,614,138 alleles · rare exomes 12,495/1,461,886 · genomes 943/152,252 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.979%	102
Remaining individualsnot grpmax-eligible	0.813%	123
Middle Eastern	0.775%	129
South Asian	0.719%	139
Admixed American	0.681%	147
Ashkenazi Jewishnot grpmax-eligible	0.405%	247
African / African-American	0.147%	682
Finnishnot grpmax-eligible	0.0578%	1,730
East Asian	0.00446%	22,442

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: SLX4
Protein: p.Ser30=
Coding: c.90C>T
MANE Select: NM_032444
dbSNP: rs118089506
Type: single nucleotide variant
Location: chr16:3608875 (GRCh38)
Gene constraint: LOEUF 0.896 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 47.20 · 7 PDB
Residue 30: the 'interaction with slx4ip, ercc4/xpf and msh2' region; the 'disordered' region

Full SLX4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Fanconi anemia complementation group P — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Fanconi anemia

Similar variants

SLX4 p.Ser30Phe Uncertain significance ★ ⚠ same residue
SLX4 c.1684-1G>A Likely pathogenic ★★ same condition
SLX4 c.951-1G>T Likely pathogenic ★★ same condition
SLX4 p.Arg1666Ter Pathogenic/Likely pathogenic ★★ same condition
SLX4 p.Arg481Ter Pathogenic/Likely pathogenic ★★ same condition
SLX4 p.Arg713Ter Pathogenic/Likely pathogenic ★★ same condition
SLX4 p.Gln1201Ter Pathogenic/Likely pathogenic ★★ same condition
SLX4 p.Gln1306Ter 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/slx4-p-ser30 (accessed [today's date]).

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