Is RTEL1 p.Ser1041= (c.3123C>T) pathogenic?

RTEL1 p.Ser1041= (c.3123C>T) is classified Likely benign in RTEL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-04). No allele count reported in gnomAD v4.1 (AN 1,604,374); Associated with dyskeratosis congenita, autosomal recessive 5.

What condition is associated with RTEL1 p.Ser1041= (c.3123C>T)?

RTEL1 p.Ser1041= (c.3123C>T) is associated with dyskeratosis congenita, autosomal recessive 5, pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 (ClinVar).

How common is RTEL1 p.Ser1041= (c.3123C>T) in the general population?

RTEL1 p.Ser1041= (c.3123C>T) is no allele count reported in gnomAD v4.1 (AN 1,604,374) (gnomAD).

RTEL1 p.Ser1041=

c.3123C>T · rs2517197601 · VCV2937491

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,604,374)

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 0.4	GERP -2.1
Overall
CADD	4.557	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,604,374). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: RTEL1
Protein: p.Ser1041=
Coding: c.3123C>T
MANE Select: NM_001283009
dbSNP: rs2517197601
Type: single nucleotide variant
Location: chr20:63694754 (GRCh38)
Gene constraint: LOEUF 0.661 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.64 · 3 PDB
Residue 1041: the 'disordered' region

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

Similar variants

RTEL1 p.Ser1041Arg Uncertain significance ★ ⚠ same residue
RTEL1 p.Ser1041Asn Uncertain significance ★ ⚠ same residue
RTEL1 p.Ser1041Gly Uncertain significance ★ ⚠ same residue
RTEL1 p.Ser1041Thr Uncertain significance ★ ⚠ same residue
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

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-ser1041 (accessed [today's date]).

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