Is RTEL1 p.Arg979= (c.2937G>A) pathogenic?

RTEL1 p.Arg979= (c.2937G>A) is classified Likely benign in RTEL1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-12-10). Very rare (popmax 0.0022%, sas); Associated with Inborn genetic diseases.

How common is RTEL1 p.Arg979= (c.2937G>A) in the general population?

RTEL1 p.Arg979= (c.2937G>A) is very rare (popmax 0.0022%, sas) (gnomAD).

RTEL1 p.Arg979=

Q: What condition is associated with RTEL1 p.Arg979= (c.2937G>A)?

RTEL1 p.Arg979= (c.2937G>A) is associated with Inborn genetic diseases, dyskeratosis congenita, autosomal recessive 5, pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 (ClinVar).

c.2937G>A · rs768689934 · VCV1152118

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

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 0.012	GERP 1.2
Overall
CADD	2.823	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,092 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000136%

Overall 0.00031% 5/1,611,980 alleles · very rare exomes 3/1,459,920 · genomes 2/152,060 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,546
Admixed American	0.00167%	59,956
European (non-Finnish)	0.00017%	589,758

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.Arg979=
Coding: c.2937G>A
MANE Select: NM_001283009
dbSNP: rs768689934
Type: single nucleotide variant
Location: chr20:63693228 (GRCh38)
Gene constraint: LOEUF 0.661 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.64 · 3 PDB
Residue 979: the 'disordered' region

Full RTEL1 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: dyskeratosis congenita, autosomal recessive 5 pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3

Similar variants

RTEL1 p.Arg979Trp Uncertain significance ★★ ⚠ same residue
RTEL1 p.Arg979Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
RTEL1 p.Arg979Leu Uncertain significance ★ ⚠ same residue
RTEL1 p.Arg979Pro 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-arg979 (accessed [today's date]).

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