# NM_007294.4(BRCA1):c.4989G>T (p.Met1663Ile)

https://sugi.bio/variant/brca1-p-met1663ile

## Summary

**BRCA1 p.Met1663Ile (c.4989G>T)** is classified **Uncertain significance** in BRCA1 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2020-03-02). AlphaMissense: likely benign (0.247); Very rare (popmax 0.000137%); Associated with breast-ovarian cancer, familial, susceptibility to, 1.

**At a glance:** Uncertain significance · review: No assertion criteria · rsID rs748807039 · 2 submitters · 1 linked condition · AlphaMissense likely benign · very rare (popmax 0.000137%)

## For patients & families {#patients}

This is a change in the BRCA1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters, and is linked to breast-ovarian cancer, familial, susceptibility to, 1.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant |
| Age of onset (of this condition) | Adult, Elderly |
| Diagnostic panels | BRCA1 is a diagnostic-grade gene on 25 Genomics England panels |

**Commonly reported features of Hereditary breast and/or ovarian cancer syndrome** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Abnormality of the fallopian tube — Very frequent (99-80%)
- Primary peritoneal carcinoma — Very frequent (99-80%)
- Ovarian neoplasm — Very frequent (99-80%)
- Breast carcinoma — Frequent (79-30%)
- Melanoma — Occasional (29-5%)
- Neoplasm of the pancreas — Occasional (29-5%)
- Prostate cancer — Occasional (29-5%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0027801/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [BRCA1](https://sugi.bio/atlas/gene/BRCA1/) |
| Protein change (HGVS p.) | p.Met1663Ile |
| Coding change (HGVS c.) | c.4989G>T |
| MANE Select transcript | [NM_007294](https://www.ncbi.nlm.nih.gov/nuccore/NM_007294) |
| dbSNP | [rs748807039](https://www.ncbi.nlm.nih.gov/snp/rs748807039/) |
| Variant type | single nucleotide variant |
| Location | chr17:43067693-43067693 (GRCh38) |
| ClinVar | [VCV868099](https://www.ncbi.nlm.nih.gov/clinvar/variation/868099/) |

**All HGVS expressions:** `LRG_292:g.150291G>T`, `LRG_292t1:c.4989G>T`, `NC_000017.10:g.41219710C>A`, `NC_000017.11:g.43067693C>A`, `NG_005905.2:g.150291G>T`, `NM_001407571.1:c.4776G>T`, `NM_001407581.1:c.5055G>T`, `NM_001407582.1:c.5055G>T`, `NM_001407583.1:c.5052G>T`, `NM_001407585.1:c.5052G>T`, `NM_001407587.1:c.5052G>T`, `NM_001407590.1:c.5049G>T`, `NM_001407591.1:c.5049G>T`, `NM_001407593.1:c.4989G>T`, `NM_001407594.1:c.4989G>T`, `NM_001407596.1:c.4989G>T`, `NM_001407597.1:c.4989G>T`, `NM_001407598.1:c.4989G>T`, `NM_001407602.1:c.4989G>T`, `NM_001407603.1:c.4989G>T`, `NM_001407605.1:c.4989G>T`, `NM_001407610.1:c.4986G>T`, `NM_001407611.1:c.4986G>T`, `NM_001407612.1:c.4986G>T`, `NM_001407613.1:c.4986G>T`, `NM_001407614.1:c.4986G>T`, `NM_001407615.1:c.4986G>T`, `NM_001407616.1:c.4986G>T`, `NM_001407617.1:c.4986G>T`, `NM_001407618.1:c.4986G>T`, `NM_001407619.1:c.4986G>T`, `NM_001407620.1:c.4986G>T`, `NM_001407621.1:c.4986G>T`, `NM_001407622.1:c.4986G>T`, `NM_001407623.1:c.4986G>T`, `NM_001407624.1:c.4986G>T`, `NM_001407625.1:c.4986G>T`, `NM_001407626.1:c.4986G>T`, `NM_001407627.1:c.4983G>T`, `NM_001407628.1:c.4983G>T`, `NM_001407629.1:c.4983G>T`, `NM_001407630.1:c.4983G>T`, `NM_001407631.1:c.4983G>T`, `NM_001407632.1:c.4983G>T`, `NM_001407633.1:c.4983G>T`, `NM_001407634.1:c.4983G>T`, `NM_001407635.1:c.4983G>T`, `NM_001407636.1:c.4983G>T`, `NM_001407637.1:c.4983G>T`, `NM_001407638.1:c.4983G>T`, `NM_001407639.1:c.4983G>T`, `NM_001407640.1:c.4983G>T`, `NM_001407641.1:c.4983G>T`, `NM_001407642.1:c.4983G>T`, `NM_001407644.1:c.4980G>T`, `NM_001407645.1:c.4980G>T`, `NM_001407646.1:c.4977G>T`, `NM_001407647.1:c.4974G>T`, `NM_001407648.1:c.4932G>T`, `NM_001407649.1:c.4929G>T`, `NM_001407652.1:c.4989G>T`, `NM_001407653.1:c.4911G>T`, `NM_001407654.1:c.4911G>T`, `NM_001407655.1:c.4911G>T`, `NM_001407656.1:c.4908G>T`, `NM_001407657.1:c.4908G>T`, `NM_001407658.1:c.4908G>T`, `NM_001407659.1:c.4905G>T`, `NM_001407660.1:c.4905G>T`, `NM_001407661.1:c.4905G>T`, `NM_001407662.1:c.4905G>T`, `NM_001407663.1:c.4905G>T`, `NM_001407664.1:c.4866G>T`, `NM_001407665.1:c.4866G>T`, `NM_001407666.1:c.4866G>T`, `NM_001407667.1:c.4866G>T`, `NM_001407668.1:c.4866G>T`, `NM_001407669.1:c.4866G>T`, `NM_001407670.1:c.4863G>T`, `NM_001407671.1:c.4863G>T`, `NM_001407672.1:c.4863G>T`, `NM_001407673.1:c.4863G>T`, `NM_001407674.1:c.4863G>T`, `NM_001407675.1:c.4863G>T`, `NM_001407676.1:c.4863G>T`, `NM_001407677.1:c.4863G>T`, `NM_001407678.1:c.4863G>T`, `NM_001407679.1:c.4863G>T`, `NM_001407680.1:c.4863G>T`, `NM_001407681.1:c.4860G>T`, `NM_001407682.1:c.4860G>T`, `NM_001407683.1:c.4860G>T`, `NM_001407684.1:c.4989G>T`, `NM_001407685.1:c.4860G>T`, `NM_001407686.1:c.4860G>T`, `NM_001407687.1:c.4860G>T`, `NM_001407688.1:c.4860G>T`, `NM_001407689.1:c.4860G>T`, `NM_001407690.1:c.4857G>T`, `NM_001407691.1:c.4857G>T`, `NM_001407692.1:c.4848G>T`, `NM_001407694.1:c.4848G>T`, `NM_001407695.1:c.4848G>T`, `NM_001407696.1:c.4848G>T`, `NM_001407697.1:c.4848G>T`, `NM_001407698.1:c.4848G>T`, `NM_001407724.1:c.4848G>T`, `NM_001407725.1:c.4848G>T`, `NM_001407726.1:c.4848G>T`, `NM_001407727.1:c.4848G>T`, `NM_001407728.1:c.4848G>T`, `NM_001407729.1:c.4848G>T`, `NM_001407730.1:c.4848G>T`, `NM_001407731.1:c.4848G>T`, `NM_001407732.1:c.4845G>T`, `NM_001407733.1:c.4845G>T`, `NM_001407734.1:c.4845G>T`, `NM_001407735.1:c.4845G>T`, `NM_001407736.1:c.4845G>T`, `NM_001407737.1:c.4845G>T`, `NM_001407738.1:c.4845G>T`, `NM_001407739.1:c.4845G>T`, `NM_001407740.1:c.4845G>T`, `NM_001407741.1:c.4845G>T`, `NM_001407742.1:c.4845G>T`, `NM_001407743.1:c.4845G>T`, `NM_001407744.1:c.4845G>T`, `NM_001407745.1:c.4845G>T`, `NM_001407746.1:c.4845G>T`, `NM_001407747.1:c.4845G>T`, `NM_001407748.1:c.4845G>T`, `NM_001407749.1:c.4845G>T`, `NM_001407750.1:c.4845G>T`, `NM_001407751.1:c.4845G>T`, `NM_001407752.1:c.4845G>T`, `NM_001407838.1:c.4842G>T`, `NM_001407839.1:c.4842G>T`, `NM_001407841.1:c.4842G>T`, `NM_001407842.1:c.4842G>T`, `NM_001407843.1:c.4842G>T`, `NM_001407844.1:c.4842G>T`, `NM_001407845.1:c.4842G>T`, `NM_001407846.1:c.4842G>T`, `NM_001407847.1:c.4842G>T`, `NM_001407848.1:c.4842G>T`, `NM_001407849.1:c.4842G>T`, `NM_001407850.1:c.4842G>T`, `NM_001407851.1:c.4842G>T`, `NM_001407852.1:c.4842G>T`, `NM_001407853.1:c.4842G>T`, `NM_001407854.1:c.4989G>T`, `NM_001407858.1:c.4986G>T`, `NM_001407859.1:c.4986G>T`, `NM_001407860.1:c.4986G>T`, `NM_001407861.1:c.4983G>T`, `NM_001407862.1:c.4788G>T`, `NM_001407863.1:c.4863G>T`, `NM_001407874.1:c.4782G>T`, `NM_001407875.1:c.4782G>T`, `NM_001407879.1:c.4779G>T`, `NM_001407881.1:c.4779G>T`, `NM_001407882.1:c.4779G>T`, `NM_001407884.1:c.4779G>T`, `NM_001407885.1:c.4779G>T`, `NM_001407886.1:c.4779G>T`, `NM_001407887.1:c.4779G>T`, `NM_001407889.1:c.4779G>T`, `NM_001407894.1:c.4776G>T`, `NM_001407895.1:c.4776G>T`, `NM_001407896.1:c.4776G>T`, `NM_001407897.1:c.4776G>T`, `NM_001407898.1:c.4776G>T`, `NM_001407899.1:c.4776G>T`, `NM_001407900.1:c.4776G>T`, `NM_001407902.1:c.4776G>T`, `NM_001407904.1:c.4776G>T`, `NM_001407906.1:c.4776G>T`, `NM_001407907.1:c.4776G>T`, `NM_001407908.1:c.4776G>T`, `NM_001407909.1:c.4776G>T`, `NM_001407910.1:c.4776G>T`, `NM_001407915.1:c.4773G>T`, `NM_001407916.1:c.4773G>T`, `NM_001407917.1:c.4773G>T`, `NM_001407918.1:c.4773G>T`, `NM_001407919.1:c.4866G>T`, `NM_001407920.1:c.4725G>T`, `NM_001407921.1:c.4725G>T`, `NM_001407922.1:c.4725G>T`, `NM_001407923.1:c.4725G>T`, `NM_001407924.1:c.4725G>T`, `NM_001407925.1:c.4725G>T`, `NM_001407926.1:c.4725G>T`, `NM_001407927.1:c.4722G>T`, `NM_001407928.1:c.4722G>T`, `NM_001407929.1:c.4722G>T`, `NM_001407930.1:c.4722G>T`, `NM_001407931.1:c.4722G>T`, `NM_001407932.1:c.4722G>T`, `NM_001407933.1:c.4722G>T`, `NM_001407934.1:c.4719G>T`, `NM_001407935.1:c.4719G>T`, `NM_001407936.1:c.4719G>T`, `NM_001407937.1:c.4866G>T`, `NM_001407938.1:c.4866G>T`, `NM_001407939.1:c.4863G>T`, `NM_001407940.1:c.4863G>T`, `NM_001407941.1:c.4860G>T`, `NM_001407942.1:c.4848G>T`, `NM_001407943.1:c.4845G>T`, `NM_001407944.1:c.4845G>T`, `NM_001407945.1:c.4845G>T`, `NM_001407946.1:c.4656G>T`, `NM_001407947.1:c.4656G>T`, `NM_001407948.1:c.4656G>T`, `NM_001407949.1:c.4656G>T`, `NM_001407950.1:c.4653G>T`, `NM_001407951.1:c.4653G>T`, `NM_001407952.1:c.4653G>T`, `NM_001407953.1:c.4653G>T`, `NM_001407954.1:c.4653G>T`, `NM_001407955.1:c.4653G>T`, `NM_001407956.1:c.4650G>T`, `NM_001407957.1:c.4650G>T`, `NM_001407958.1:c.4650G>T`, `NM_001407959.1:c.4608G>T`, `NM_001407960.1:c.4605G>T`, `NM_001407962.1:c.4605G>T`, `NM_001407963.1:c.4602G>T`, `NM_001407964.1:c.4527G>T`, `NM_001407965.1:c.4482G>T`, `NM_001407966.1:c.4101G>T`, `NM_001407967.1:c.4098G>T`, `NM_001407968.1:c.2385G>T`, `NM_001407969.1:c.2382G>T`, `NM_001407970.1:c.1746G>T`, `NM_001407971.1:c.1746G>T`, `NM_001407972.1:c.1743G>T`, `NM_001407973.1:c.1680G>T`, `NM_001407974.1:c.1680G>T`, `NM_001407975.1:c.1680G>T`, `NM_001407976.1:c.1680G>T`, `NM_001407977.1:c.1680G>T`, `NM_001407978.1:c.1680G>T`, `NM_001407979.1:c.1677G>T`, `NM_001407980.1:c.1677G>T`, `NM_001407981.1:c.1677G>T`, `NM_001407982.1:c.1677G>T`, `NM_001407983.1:c.1677G>T`, `NM_001407984.1:c.1677G>T`, `NM_001407985.1:c.1677G>T`, `NM_001407986.1:c.1677G>T`, `NM_001407990.1:c.1677G>T`, `NM_001407991.1:c.1677G>T`, `NM_001407992.1:c.1677G>T`, `NM_001407993.1:c.1677G>T`, `NM_001408392.1:c.1674G>T`, `NM_001408396.1:c.1674G>T`, `NM_001408397.1:c.1674G>T`, `NM_001408398.1:c.1674G>T`, `NM_001408399.1:c.1674G>T`, `NM_001408400.1:c.1674G>T`, `NM_001408401.1:c.1674G>T`, `NM_001408402.1:c.1674G>T`, `NM_001408403.1:c.1674G>T`, `NM_001408404.1:c.1674G>T`, `NM_001408406.1:c.1671G>T`, `NM_001408407.1:c.1671G>T`, `NM_001408408.1:c.1671G>T`, `NM_001408409.1:c.1668G>T`, `NM_001408410.1:c.1605G>T`, `NM_001408411.1:c.1602G>T`, `NM_001408412.1:c.1599G>T`, `NM_001408413.1:c.1599G>T`, `NM_001408414.1:c.1599G>T`, `NM_001408415.1:c.1599G>T`, `NM_001408416.1:c.1599G>T`, `NM_001408418.1:c.1563G>T`, `NM_001408419.1:c.1563G>T`, `NM_001408420.1:c.1563G>T`, `NM_001408421.1:c.1560G>T`, `NM_001408422.1:c.1560G>T`, `NM_001408423.1:c.1560G>T`, `NM_001408424.1:c.1560G>T`, `NM_001408425.1:c.1557G>T`, `NM_001408426.1:c.1557G>T`, `NM_001408427.1:c.1557G>T`, `NM_001408428.1:c.1557G>T`, `NM_001408429.1:c.1557G>T`, `NM_001408430.1:c.1557G>T`, `NM_001408431.1:c.1557G>T`, `NM_001408432.1:c.1554G>T`, `NM_001408433.1:c.1554G>T`, `NM_001408434.1:c.1554G>T`, `NM_001408435.1:c.1554G>T`, `NM_001408436.1:c.1554G>T`, `NM_001408437.1:c.1554G>T`, `NM_001408438.1:c.1554G>T`, `NM_001408439.1:c.1554G>T`, `NM_001408440.1:c.1554G>T`, `NM_001408441.1:c.1554G>T`, `NM_001408442.1:c.1554G>T`, `NM_001408443.1:c.1554G>T`, `NM_001408444.1:c.1554G>T`, `NM_001408445.1:c.1551G>T`, `NM_001408446.1:c.1551G>T`, `NM_001408447.1:c.1551G>T`, `NM_001408448.1:c.1551G>T`, `NM_001408450.1:c.1551G>T`, `NM_001408451.1:c.1545G>T`, `NM_001408452.1:c.1539G>T`, `NM_001408453.1:c.1539G>T`, `NM_001408454.1:c.1539G>T`, `NM_001408455.1:c.1539G>T`, `NM_001408456.1:c.1539G>T`, `NM_001408457.1:c.1539G>T`, `NM_001408458.1:c.1536G>T`, `NM_001408459.1:c.1536G>T`, `NM_001408460.1:c.1536G>T`, `NM_001408461.1:c.1536G>T`, `NM_001408462.1:c.1536G>T`, `NM_001408463.1:c.1536G>T`, `NM_001408464.1:c.1536G>T`, `NM_001408465.1:c.1536G>T`, `NM_001408466.1:c.1536G>T`, `NM_001408467.1:c.1536G>T`, `NM_001408468.1:c.1533G>T`, `NM_001408469.1:c.1533G>T`, `NM_001408470.1:c.1533G>T`, `NM_001408472.1:c.1677G>T`, `NM_001408473.1:c.1674G>T`, `NM_001408474.1:c.1479G>T`, `NM_001408475.1:c.1476G>T`, `NM_001408476.1:c.1476G>T`, `NM_001408478.1:c.1470G>T`, `NM_001408479.1:c.1470G>T`, `NM_001408480.1:c.1470G>T`, `NM_001408481.1:c.1467G>T`, `NM_001408482.1:c.1467G>T`, `NM_001408483.1:c.1467G>T`, `NM_001408484.1:c.1467G>T`, `NM_001408485.1:c.1467G>T`, `NM_001408489.1:c.1467G>T`, `NM_001408490.1:c.1467G>T`, `NM_001408491.1:c.1467G>T`, `NM_001408492.1:c.1464G>T`, `NM_001408493.1:c.1464G>T`, `NM_001408494.1:c.1440G>T`, `NM_001408495.1:c.1434G>T`, `NM_001408496.1:c.1416G>T`, `NM_001408497.1:c.1416G>T`, `NM_001408498.1:c.1416G>T`, `NM_001408499.1:c.1416G>T`, `NM_001408500.1:c.1416G>T`, `NM_001408501.1:c.1416G>T`, `NM_001408502.1:c.1413G>T`, `NM_001408503.1:c.1413G>T`, `NM_001408504.1:c.1413G>T`, `NM_001408505.1:c.1410G>T`, `NM_001408506.1:c.1353G>T`, `NM_001408507.1:c.1350G>T`, `NM_001408508.1:c.1341G>T`, `NM_001408509.1:c.1338G>T`, `NM_001408510.1:c.1299G>T`, `NM_001408511.1:c.1296G>T`, `NM_001408512.1:c.1176G>T`, `NM_001408513.1:c.1149G>T`, `NM_007294.4:c.4989G>T`, `NM_007297.4:c.4848G>T`, `NM_007298.4:c.1677G>T`, `NM_007299.4:c.1677G>T`, `NM_007300.4:c.5052G>T`, `NM_007304.2:c.1677G>T`, `NR_027676.2:n.5166G>T`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.247)
- REVEL 0.559 (indeterminate)
- SaProt LLR -6.052 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this tolerated; REVEL makes no call
- Conservation: phyloP 0.261, GERP -0.432, phastCons 0.35 — weakly conserved position
- CADD: **PHRED 16.26**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 0.91** across the covering region of the MANE Select transcript (43,045,681–43,124,096), spanning 78,415 bp. Chi-square p 4.8e-05. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): global (via dbSNP) **0.000137%** · 2/1,457,624 alleles overall — very rare (popmax 0.000137%).

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**BRCA1** population constraint: LOEUF 0.885, pLI 1.5474e-34, missense-Z 2.3379; ClinGen dosage — haploinsufficiency 3, triplosensitivity 0 (0–3 scale). *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **BRCA1-related cancer predisposition** — Definitive (AD)
- **Fanconi anemia, complementation group S** — Definitive (AR)

## Protein context {#protein}

Residue **1663** lies in the brct 1 domain; a UniProt-annotated variant site (in fancs); an α-helix.

AlphaFold model confidence (whole protein): pLDDT 41.99, 11% of residues very-high.

**33 experimental structure(s)** (PDB): [1JM7](https://www.rcsb.org/structure/1JM7), [1JNX](https://www.rcsb.org/structure/1JNX), [1N5O](https://www.rcsb.org/structure/1N5O), [1OQA](https://www.rcsb.org/structure/1OQA), [1T15](https://www.rcsb.org/structure/1T15), [1T29](https://www.rcsb.org/structure/1T29) — incl. mutant structure 1T2U.

## What this gene does {#gene-function}

*Describes the biological roles of BRCA1 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** BRCA1's established molecular role includes transcription cis-regulatory region binding. p.Met1663Ile falls in the brct 1 domain. In Reactome, BRCA1 is annotated in disease pathway(s) including **Defective DNA double strand break response due to BARD1 loss of function**, **Defective DNA double strand break response due to BRCA1 loss of function**.

**Disease mechanism (Reactome):** BRCA1 loss or alteration is curated in [Defective DNA double strand break response due to BARD1 loss of function](https://reactome.org/content/detail/R-HSA-9699150), [Defective DNA double strand break response due to BRCA1 loss of function](https://reactome.org/content/detail/R-HSA-9663199), [Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function](https://reactome.org/content/detail/R-HSA-9704331).

### Pathways affected {#pathways}

BRCA1 participates in **28 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective DNA double strand break response due to BARD1 loss of function](https://reactome.org/content/detail/R-HSA-9699150) | curated |
| ⚕ [Defective DNA double strand break response due to BRCA1 loss of function](https://reactome.org/content/detail/R-HSA-9663199) | curated |
| ⚕ [Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function](https://reactome.org/content/detail/R-HSA-9704331) | curated |
| ⚕ [Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function](https://reactome.org/content/detail/R-HSA-9704646) | curated |
| ⚕ [Defective homologous recombination repair (HRR) due to BRCA1 loss of function](https://reactome.org/content/detail/R-HSA-9701192) | curated |
| ⚕ [Impaired BRCA2 binding to PALB2](https://reactome.org/content/detail/R-HSA-9709603) | curated |
| ⚕ [Impaired BRCA2 binding to RAD51](https://reactome.org/content/detail/R-HSA-9709570) | curated |
| [G2/M DNA damage checkpoint](https://reactome.org/content/detail/R-HSA-69473) | curated |
| [HDR through Homologous Recombination (HRR)](https://reactome.org/content/detail/R-HSA-5685942) | curated |
| [HDR through Single Strand Annealing (SSA)](https://reactome.org/content/detail/R-HSA-5685938) | curated |
| [Homologous DNA Pairing and Strand Exchange](https://reactome.org/content/detail/R-HSA-5693579) | curated |
| [KEAP1-NFE2L2 pathway](https://reactome.org/content/detail/R-HSA-9755511) | curated |
| [Metalloprotease DUBs](https://reactome.org/content/detail/R-HSA-5689901) | curated |
| [Neddylation](https://reactome.org/content/detail/R-HSA-8951664) | curated |
| [Negative Regulation of DNA Double Strand Break Response](https://reactome.org/content/detail/R-HSA-9974237) | curated |
| [Nonhomologous End-Joining (NHEJ)](https://reactome.org/content/detail/R-HSA-5693571) | curated |
| [Presynaptic phase of homologous DNA pairing and strand exchange](https://reactome.org/content/detail/R-HSA-5693616) | curated |
| [Processing of DNA double-strand break ends](https://reactome.org/content/detail/R-HSA-5693607) | curated |
| [Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks](https://reactome.org/content/detail/R-HSA-5693565) | curated |
| [Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence](https://reactome.org/content/detail/R-HSA-9825895) | curated |
| [Regulation of TP53 Activity through Phosphorylation](https://reactome.org/content/detail/R-HSA-6804756) | curated |
| [Resolution of D-loop Structures through Holliday Junction Intermediates](https://reactome.org/content/detail/R-HSA-5693568) | curated |
| [Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)](https://reactome.org/content/detail/R-HSA-5693554) | curated |
| [SUMOylation of DNA damage response and repair proteins](https://reactome.org/content/detail/R-HSA-3108214) | curated |
| [TP53 Regulates Transcription of DNA Repair Genes](https://reactome.org/content/detail/R-HSA-6796648) | curated |
| [Transcriptional Regulation by E2F6](https://reactome.org/content/detail/R-HSA-8953750) | curated |
| [Meiotic recombination](https://reactome.org/content/detail/R-HSA-912446) | electronic |
| [Meiotic synapsis](https://reactome.org/content/detail/R-HSA-1221632) | electronic |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** transcription cis-regulatory region binding, p53 binding, transcription coactivator activity, RNA binding, ubiquitin-protein transferase activity, enzyme binding.

**Biological process:** double-strand break repair via homologous recombination, DNA damage tolerance, double-strand break repair, regulation of transcription by RNA polymerase II, chromosome segregation, mitotic G2 DNA damage checkpoint signaling.

## Clinical significance {#significance}

**Uncertain significance** — review status No assertion criteria *(no assertion criteria provided)*, last evaluated 2020-03-02.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

**Submission history:** 2 submissions (2020); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| BRCAlab, Lund University | Uncertain significance | no assertion criteria provided | clinical testing | 2020-03-02 |
| Brotman Baty Institute, University of Washington |  | no classification provided | in vitro |  |

## Associated conditions {#conditions}

[breast-ovarian cancer, familial, susceptibility to, 1](https://sugi.bio/atlas/disease/breast-ovarian-cancer-familial-susceptibility-to-1/).

**Reported phenotype names (ClinVar):** Breast-ovarian cancer, familial, susceptibility to, 1, BRCA1 Hereditary Breast and Ovarian Cancer, OVARIAN CANCER, SUSCEPTIBILITY TO.

## Same-residue context {#hotspot}

Residue **1663** carries **2 other pathogenic ClinVar variants** — a recurrently-mutated position: [BRCA1 p.Met1663fs](/variant/brca1-p-met1663fs), [BRCA1 p.Met1663Arg](/variant/brca1-p-met1663arg). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related BRCA1 variant pages (same residue, condition, or type): [BRCA1 p.Met1663Lys](/variant/brca1-p-met1663lys), [BRCA1 p.Met1663Arg](/variant/brca1-p-met1663arg), [BRCA1 p.Met1663Leu](/variant/brca1-p-met1663leu), [BRCA1 p.Met1663fs](/variant/brca1-p-met1663fs), [BRCA1 p.Met1663Thr](/variant/brca1-p-met1663thr), [BRCA1 c.134+3A>T](/variant/brca1-c-134-plus-3a-t), [BRCA1 c.135-1G>T](/variant/brca1-c-135-minus-1g-t), [BRCA1 c.212+1G>A](/variant/brca1-c-212-plus-1g-a).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 868099). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*