Is RTEL1 p.Cys457= (c.1371C>T) pathogenic?

RTEL1 p.Cys457= (c.1371C>T) is classified Likely benign in RTEL1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-19). Rare (popmax 0.18%, afr); Associated with dyskeratosis congenita, autosomal recessive 5.

What condition is associated with RTEL1 p.Cys457= (c.1371C>T)?

RTEL1 p.Cys457= (c.1371C>T) is associated with dyskeratosis congenita, autosomal recessive 5, pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3, dyskeratosis congenita (ClinVar).

How common is RTEL1 p.Cys457= (c.1371C>T) in the general population?

RTEL1 p.Cys457= (c.1371C>T) is rare (popmax 0.18%, afr) (gnomAD).

RTEL1 p.Cys457=

c.1371C>T · rs138399496 · VCV726399

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.18%, afr)

Conditions

dyskeratosis congenita, autosomal recessive 5

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 0.67	GERP -0.89, phastCons 1
Overall
CADD	9.117	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.18% African / African-American · 135/74,988 alleles

Filtering AF 0.155% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.146%

Overall 0.0107% 173/1,609,484 alleles · rare exomes 101/1,457,108 · genomes 72/152,376 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.18%	555
Remaining individualsnot grpmax-eligible	0.037%	2,706
Admixed American	0.015%	6,653
South Asian	0.00441%	22,676
European (non-Finnish)	0.00017%	589,713

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: RTEL1
Protein: p.Cys457=
Coding: c.1371C>T
MANE Select: NM_001283009
dbSNP: rs138399496
Type: single nucleotide variant
Location: chr20:63687660 (GRCh38)
Gene constraint: LOEUF 0.661 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.64 · 3 PDB

Full RTEL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

dyskeratosis congenita, autosomal recessive 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 dyskeratosis congenita

Similar variants

RTEL1 c.1037+1G>T Likely pathogenic ★★ same condition
RTEL1 c.1192-2A>G Likely pathogenic ★★ same condition
RTEL1 c.1596-1G>A Likely pathogenic ★★ same condition
RTEL1 c.2142-1G>C Likely pathogenic ★★ same condition
RTEL1 c.2265+1G>T Likely pathogenic ★★ same condition
RTEL1 c.2413+1G>A Likely pathogenic ★★ same condition
RTEL1 c.2413+1G>C Pathogenic/Likely pathogenic ★★ same condition
RTEL1 c.2557-2A>G 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/rtel1-p-cys457 (accessed [today's date]).

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